=>> Building biology/salmon build started at Sat May 3 16:54:18 BST 2025 port directory: /usr/ports/biology/salmon package name: salmon-1.10.2_7 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1490 Feb 16 09:27 /usr/ports/biology/salmon/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: fa53920e72 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 08 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/salmon/work/.cache HOME=/wrkdirs/usr/ports/biology/salmon/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/salmon/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/salmon/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/salmon/work/.cache HOME=/wrkdirs/usr/ports/biology/salmon/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/salmon/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/salmon/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lpthread -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/salmon" EXAMPLESDIR="share/examples/salmon" DATADIR="share/salmon" WWWDIR="www/salmon" ETCDIR="etc/salmon" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/salmon DOCSDIR=/usr/local/share/doc/salmon EXAMPLESDIR=/usr/local/share/examples/salmon WWWDIR=/usr/local/www/salmon ETCDIR=/usr/local/etc/salmon --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.2_7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> salmon-1.10.2_7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of salmon-1.10.2_7 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by salmon-1.10.2_7 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by salmon-1.10.2_7 for building => SHA256 Checksum OK for COMBINE-lab-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz. => SHA256 Checksum OK for samtools-htscodecs-5aecc6e_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by salmon-1.10.2_7 for building ===> Extracting for salmon-1.10.2_7 => SHA256 Checksum OK for COMBINE-lab-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz. => SHA256 Checksum OK for samtools-htscodecs-5aecc6e_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for salmon-1.10.2_7 ===> Applying FreeBSD patches for salmon-1.10.2_7 from /usr/ports/biology/salmon/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.2_7 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.37.pkg [pkg-builder.dan.net.uk] Installing bash-5.2.37... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting bash-5.2.37: .......... done ===> salmon-1.10.2_7 depends on executable: bash - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on package: cereal>=1.3.0 - not found ===> Installing existing package /packages/All/cereal-1.3.2_1.pkg [pkg-builder.dan.net.uk] Installing cereal-1.3.2_1... [pkg-builder.dan.net.uk] `-- Installing boost-libs-1.87.0_1... [pkg-builder.dan.net.uk] | `-- Installing icu-76.1,1... [pkg-builder.dan.net.uk] | `-- Extracting icu-76.1,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting boost-libs-1.87.0_1: .......... done [pkg-builder.dan.net.uk] Extracting cereal-1.3.2_1: .......... done ===== Message from boost-libs-1.87.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> salmon-1.10.2_7 depends on package: cereal>=1.3.0 - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on package: libgff==2.0.0 - not found ===> Installing existing package /packages/All/libgff-2.0.0.pkg [pkg-builder.dan.net.uk] Installing libgff-2.0.0... [pkg-builder.dan.net.uk] Extracting libgff-2.0.0: .......... done ===> salmon-1.10.2_7 depends on package: libgff==2.0.0 - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on executable: libtool - not found ===> Installing existing package /packages/All/libtool-2.5.4.pkg [pkg-builder.dan.net.uk] Installing libtool-2.5.4... [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] Extracting libtool-2.5.4: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> salmon-1.10.2_7 depends on executable: libtool - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on executable: autoreconf - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg-builder.dan.net.uk] Installing autoconf-2.72... [pkg-builder.dan.net.uk] `-- Installing autoconf-switch-20220527... [pkg-builder.dan.net.uk] `-- Extracting autoconf-switch-20220527: ....... done [pkg-builder.dan.net.uk] `-- Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_3: .......... done [pkg-builder.dan.net.uk] Extracting autoconf-2.72: .......... done ===> salmon-1.10.2_7 depends on executable: autoreconf - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on executable: aclocal - not found ===> Installing existing package /packages/All/automake-1.17.pkg [pkg-builder.dan.net.uk] Installing automake-1.17... [pkg-builder.dan.net.uk] Extracting automake-1.17: .......... done ===> salmon-1.10.2_7 depends on executable: aclocal - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.6.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.31.6... [pkg-builder.dan.net.uk] `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.6_1... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.51.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.51.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.31.6: .......... done ===> salmon-1.10.2_7 depends on file: /usr/local/bin/cmake - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> salmon-1.10.2_7 depends on package: gmake>=4.4.1 - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> salmon-1.10.2_7 depends on file: /usr/local/bin/ccache - found ===> Returning to build of salmon-1.10.2_7 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.2_7 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> salmon-1.10.2_7 depends on shared library: libtbb.so - not found ===> Installing existing package /packages/All/onetbb-2022.1.0.pkg [pkg-builder.dan.net.uk] Installing onetbb-2022.1.0... [pkg-builder.dan.net.uk] `-- Installing hwloc2-2.11.2... [pkg-builder.dan.net.uk] | `-- Installing level-zero-1.21.9... [pkg-builder.dan.net.uk] | | `-- Installing libfmt-10.2.1... [pkg-builder.dan.net.uk] | | `-- Extracting libfmt-10.2.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing spdlog-1.15.2... [pkg-builder.dan.net.uk] | | `-- Extracting spdlog-1.15.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting level-zero-1.21.9: .......... done [pkg-builder.dan.net.uk] | `-- Installing libpciaccess-0.18.1_1... [pkg-builder.dan.net.uk] | | `-- Installing hwdata-0.394,1... [pkg-builder.dan.net.uk] | | `-- Extracting hwdata-0.394,1: ...... done [pkg-builder.dan.net.uk] | `-- Extracting libpciaccess-0.18.1_1: ..... done [pkg-builder.dan.net.uk] | `-- Installing libxml2-2.11.9... [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libxml2-2.11.9: .......... done [pkg-builder.dan.net.uk] `-- Extracting hwloc2-2.11.2: .......... done [pkg-builder.dan.net.uk] Extracting onetbb-2022.1.0: .......... done ===> salmon-1.10.2_7 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so) ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-8.13.0_1.pkg [pkg-builder.dan.net.uk] Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] Extracting curl-8.13.0_1: .......... done ===> salmon-1.10.2_7 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of salmon-1.10.2_7 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for salmon-1.10.2_7 (cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && ./bootstrap) + rm -rf install-sh missing mkinstalldirs depcomp aclocal.m4 config.cache config.log config.status configure autom4te.cache io_lib_config.h.in config.sub config.guess Makefile.in progs/Makefile.in progs/Makefile read/Makefile.in read/Makefile tests/Makefile tests/Makefile.in io_lib-config + autoreconf -i libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:81: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:81: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:81: the top level configure.ac:101: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:101: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from... configure.ac:101: the top level configure.ac:102: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:102: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:156: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:156: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_libdeflate.m4:31: AX_LIBDEFLATE is expanded from... configure.ac:156: the top level configure.ac:157: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:157: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_zstd.m4:31: AX_ZSTD is expanded from... configure.ac:157: the top level configure.ac:190: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:190: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:190: the top level configure.ac:255: warning: AC_OUTPUT should be used without arguments. configure.ac:255: You should run autoupdate. configure.ac:79: installing './compile' configure.ac:81: installing './config.guess' configure.ac:81: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' io_lib/Makefile.am: installing './depcomp' + cd htscodecs + autoreconf -i libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' parallel-tests: installing '../test-driver' ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/salmon/work/.build CC: gcc CC version: -- The C compiler identification is Clang 18.1.6 -- The CXX compiler identification is Clang 18.1.6 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Detected non-ARM host. Setting USE_ARM to false. version: 1.10.2 -- CMAKE_BUILD_TYPE = Release -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Performing Test HAVE_LIBCPP -- Performing Test HAVE_LIBCPP - Success It appears that you're compiling with clang and that libc++ is available, so I'll use that Making Release build setting -DHAVE_NUMERIC_LIMITS128 CMake Warning (dev) at CMakeLists.txt:316 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. running /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/scripts/fetchPufferfish.sh 2>&1 -- fetch PUFFERFISH exit code 0 -- Found ZLIB: /usr/lib/libz.a (found version "1.3.1") -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: built in to C library Found liblzma library: /usr/lib/liblzma.a;/usr/lib/libmd.a =========================================== -- Found BZip2: /usr/lib/libbz2.a (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found Found libbz2 library: /usr/lib/libbz2.a =========================================== CMake Warning (dev) at CMakeLists.txt:438 (find_package): Policy CMP0144 is not set: find_package uses upper-case _ROOT variables. Run "cmake --help-policy CMP0144" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMake variable BOOST_ROOT is set to: /usr/local For compatibility, find_package is ignoring the variable, but code in a .cmake module might still use it. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:438 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/local/include (found suitable version "1.87.0", minimum required is "1.59.0") found components: iostreams system filesystem timer chrono program_options regex BOOST_INCLUDEDIR = BOOST_LIBRARYDIR = Boost_FOUND = TRUE BOOST ROOT = /usr/local BOOST INCLUDE DIR = /usr/local/include BOOST INCLUDE DIRS = /usr/local/include BOOST LIB DIR = /usr/local/lib BOOST LIBRARIES = /usr/local/lib/libboost_iostreams.a;/usr/local/lib/libboost_system.a;/usr/local/lib/libboost_filesystem.a;/usr/local/lib/libboost_timer.a;/usr/local/lib/libboost_chrono.a;/usr/local/lib/libboost_program_options.a;/usr/local/lib/libboost_regex.a -- Found cereal: /usr/local/include (found suitable version "1.3.2", minimum required is "1.3.2") -- cereal found (include: /usr/local/include) -- Found TBB: /usr/local/lib/cmake/TBB/TBBConfig.cmake (found suitable version "2022.1.0", minimum required is "2021.4") FOUND SUITABLE TBB VERSION : 2022.1.0 -- libgff ver. 2.0.0 found. -- include: /usr/local/include/ -- lib : /usr/local/lib/ -- Found CURL: /usr/local/lib/libcurl.a (found version "8.13.0") Build system will compile Staden IOLib ================================================================== CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/ CC: /usr/local/libexec/ccache/cc CC version: version: 1.0.0 Building basic pufferfish components for salmon setting -DHAVE_NUMERIC_LIMITS128 CMake Deprecation Warning at external/pufferfish/external/ntcard/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at external/pufferfish/external/twopaco/graphdump/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- setting COMPACT_VECTOR_DIR for graphdump to be /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump CMake Deprecation Warning at external/pufferfish/external/twopaco/graphconstructor/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. add library puffer : PufferfishIndexer.cpp;PufferfishBaseIndex.cpp;PufferfishIndex.cpp;PufferfishSparseIndex.cpp;PufferfishLossyIndex.cpp;edlib.cpp;Util.cpp;rank9sel.cpp;rank9b.cpp;PufferfishValidate.cpp;PufferfishStats.cpp;PufferfishTestLookup.cpp;PufferfishExamine.cpp;PufferfishKmerQuery.cpp;FastxParser.cpp;PufferfishBinaryGFAReader.cpp;PufferFS.cpp;xxhash.c;FixFasta.cpp;MemCollector.cpp;MemChainer.cpp;PuffAligner.cpp;PufferfishAligner.cpp;RefSeqConstructor.cpp;metro/metrohash64.cpp;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/LibraryFormat.cpp adding /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump to include path for libpuffer fetched path for compact_vector as [/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump] NO_IPO = FALSE TBB_LIBRARIES = TBB_LIB_INSTALL_DIR = /usr/local/lib TBBGLOBS = /usr/local/lib/libtbb.so;/usr/local/lib/libtbb.so.12;/usr/local/lib/libtbb.so.12.15;/usr/local/lib/libtbbbind_2_0.so;/usr/local/lib/libtbbbind_2_0.so.3;/usr/local/lib/libtbbbind_2_0.so.3.15;/usr/local/lib/libtbbmalloc.so;/usr/local/lib/libtbbmalloc.so.2;/usr/local/lib/libtbbmalloc.so.2.15;/usr/local/lib/libtbbmalloc_proxy.so;/usr/local/lib/libtbbmalloc_proxy.so.2;/usr/local/lib/libtbbmalloc_proxy.so.2.15 -- Configuring done (2.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED FETCHED_LIBGFF -- Build files have been written to: /wrkdirs/usr/ports/biology/salmon/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for salmon-1.10.2_7 /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 -B/wrkdirs/usr/ports/biology/salmon/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/salmon/work/.build//CMakeFiles/progress.marks /usr/local/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles/libstadenio.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 1%] Creating directories for 'libstadenio' /usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/tmp/libstadenio-mkdirs.cmake /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-mkdir [ 1%] No download step for 'libstadenio' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-download [ 2%] No update step for 'libstadenio' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-update [ 3%] No patch step for 'libstadenio' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-patch [ 4%] Performing configure step for 'libstadenio' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && ./configure --enable-shared=no --without-libcurl --prefix=/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install LDFLAGS= CFLAGS= CC=/usr/local/libexec/ccache/cc CXX=/usr/local/libexec/ccache/c++ checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 2 checking whether build environment is sane... yes checking for a race-free mkdir -p... mkdir -p checking for gawk... no checking for mawk... no checking for nawk... nawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... /usr/local/libexec/ccache/cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether /usr/local/libexec/ccache/cc accepts -g... yes checking for /usr/local/libexec/ccache/cc option to enable C11 features... none needed checking whether /usr/local/libexec/ccache/cc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of /usr/local/libexec/ccache/cc... gcc3 checking build system type... amd64-unknown-freebsd14.2 checking host system type... amd64-unknown-freebsd14.2 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by /usr/local/libexec/ccache/cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 393216 checking how to convert amd64-unknown-freebsd14.2 file names to amd64-unknown-freebsd14.2 format... func_convert_file_noop checking how to convert amd64-unknown-freebsd14.2 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking command to parse /usr/bin/nm output from /usr/local/libexec/ccache/cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if /usr/local/libexec/ccache/cc supports -fno-rtti -fno-exceptions... yes checking for /usr/local/libexec/ccache/cc option to produce PIC... -fPIC -DPIC checking if /usr/local/libexec/ccache/cc PIC flag -fPIC -DPIC works... yes checking if /usr/local/libexec/ccache/cc static flag -static works... yes checking if /usr/local/libexec/ccache/cc supports -c -o file.o... yes checking if /usr/local/libexec/ccache/cc supports -c -o file.o... (cached) yes checking whether the /usr/local/libexec/ccache/cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd14.2 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for inflateEnd in -lz... yes checking for zlib.h... yes checking for library containing gethostbyname... none required checking for library containing socket... none required checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for bsc_compress in -lbsc... no checking whether byte ordering is bigendian... no checking for egrep... (cached) /usr/bin/grep -E checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for malloc.h... yes checking for zlib.h... (cached) yes checking for stdio_ext.h... no checking whether byte ordering is bigendian... (cached) no checking size of short... 2 checking size of int... 4 checking size of long... 8 checking for inline... inline checking for mode_t... yes checking for fileno... yes checking for fstat... yes checking for mallopt... no checking for /usr/local/libexec/ccache/cc option to enable large file support... none needed checking for declarations of fseeko and ftello... yes checking for getpagesize... yes checking for working mmap... yes checking for library containing pthread_join... none required checking for library containing cos... -lm checking for strdup... yes checking for fsync... yes checking that generated files are newer than configure... done === configuring in htscodecs (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs) configure: running /bin/sh ./configure '--prefix=/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install' --disable-option-checking '--enable-shared=no' '--without-libcurl' 'LDFLAGS=' 'CFLAGS=' 'CC=/usr/local/libexec/ccache/cc' 'CXX=/usr/local/libexec/ccache/c++' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' '--disable-shared' '--with-pic' '--srcdir=.' --cache-file= checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 2 checking whether build environment is sane... yes checking for a race-free mkdir -p... mkdir -p checking for gawk... no checking for mawk... no checking for nawk... nawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... /usr/local/libexec/ccache/cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether /usr/local/libexec/ccache/cc accepts -g... yes checking for /usr/local/libexec/ccache/cc option to enable C11 features... none needed checking whether /usr/local/libexec/ccache/cc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of /usr/local/libexec/ccache/cc... gcc3 checking build system type... amd64-unknown-freebsd14.2 checking host system type... amd64-unknown-freebsd14.2 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by /usr/local/libexec/ccache/cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 393216 checking how to convert amd64-unknown-freebsd14.2 file names to amd64-unknown-freebsd14.2 format... func_convert_file_noop checking how to convert amd64-unknown-freebsd14.2 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking command to parse /usr/bin/nm output from /usr/local/libexec/ccache/cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if /usr/local/libexec/ccache/cc supports -fno-rtti -fno-exceptions... yes checking for /usr/local/libexec/ccache/cc option to produce PIC... -fPIC -DPIC checking if /usr/local/libexec/ccache/cc PIC flag -fPIC -DPIC works... yes checking if /usr/local/libexec/ccache/cc static flag -static works... yes checking if /usr/local/libexec/ccache/cc supports -c -o file.o... yes checking if /usr/local/libexec/ccache/cc supports -c -o file.o... (cached) yes checking whether the /usr/local/libexec/ccache/cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd14.2 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for __builtin_prefetch... yes checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for malloc.h... yes checking for zlib.h... yes checking for function pthread_join... -lthr checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating htscodecs/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: creating ./config.status config.status: creating Makefile config.status: creating io_lib/Makefile config.status: creating progs/Makefile config.status: creating tests/Makefile config.status: creating io_lib-config config.status: creating io_lib/os.h config.status: creating io_lib/version.h config.status: creating io_lib_config.h config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------- CONFIGURE SUMMARY -------------------------------------------------- Bzip2 enabled: yes lzma enabled: yes custom-buffering enabled: yes Using own crc: yes Libcurl enabled: no Libdeflate enabled: no have libbsc: no Have zstd: no CC: /usr/local/libexec/ccache/cc CFLAGS: -Wall LDFLAGS: LIBS: -lm -llzma -lbz2 -L/usr/local/lib cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-configure [ 5%] Performing build step for 'libstadenio' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && gmake CC=/usr/local/libexec/ccache/cc CXX=/usr/local/libexec/ccache/c++ CFLAGS+= CFLAGS+= LDFLAGS+= CFLAGS+= CFLAGS+= CFLAGS+= gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake all-recursive gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' Making all in htscodecs gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake all-recursive gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making all in htscodecs gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' Update version.h: #define HTSCODECS_VERSION_TEXT "1.5.0" gmake all-am gmake[8]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT pack.lo -MD -MP -MF .deps/pack.Tpo -c -o pack.lo pack.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT pack.lo -MD -MP -MF .deps/pack.Tpo -c pack.c -fPIC -DPIC -o pack.o mv -f .deps/pack.Tpo .deps/pack.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rle.lo -MD -MP -MF .deps/rle.Tpo -c -o rle.lo rle.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rle.lo -MD -MP -MF .deps/rle.Tpo -c rle.c -fPIC -DPIC -o rle.o mv -f .deps/rle.Tpo .deps/rle.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT fqzcomp_qual.lo -MD -MP -MF .deps/fqzcomp_qual.Tpo -c -o fqzcomp_qual.lo fqzcomp_qual.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT fqzcomp_qual.lo -MD -MP -MF .deps/fqzcomp_qual.Tpo -c fqzcomp_qual.c -fPIC -DPIC -o fqzcomp_qual.o mv -f .deps/fqzcomp_qual.Tpo .deps/fqzcomp_qual.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static.lo -MD -MP -MF .deps/rANS_static.Tpo -c -o rANS_static.lo rANS_static.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static.lo -MD -MP -MF .deps/rANS_static.Tpo -c rANS_static.c -fPIC -DPIC -o rANS_static.o mv -f .deps/rANS_static.Tpo .deps/rANS_static.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static4x16pr.lo -MD -MP -MF .deps/rANS_static4x16pr.Tpo -c -o rANS_static4x16pr.lo rANS_static4x16pr.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static4x16pr.lo -MD -MP -MF .deps/rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -fPIC -DPIC -o rANS_static4x16pr.o mv -f .deps/rANS_static4x16pr.Tpo .deps/rANS_static4x16pr.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static32x16pr.lo -MD -MP -MF .deps/rANS_static32x16pr.Tpo -c -o rANS_static32x16pr.lo rANS_static32x16pr.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static32x16pr.lo -MD -MP -MF .deps/rANS_static32x16pr.Tpo -c rANS_static32x16pr.c -fPIC -DPIC -o rANS_static32x16pr.o mv -f .deps/rANS_static32x16pr.Tpo .deps/rANS_static32x16pr.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static32x16pr_neon.lo -MD -MP -MF .deps/rANS_static32x16pr_neon.Tpo -c -o rANS_static32x16pr_neon.lo rANS_static32x16pr_neon.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static32x16pr_neon.lo -MD -MP -MF .deps/rANS_static32x16pr_neon.Tpo -c rANS_static32x16pr_neon.c -fPIC -DPIC -o rANS_static32x16pr_neon.o mv -f .deps/rANS_static32x16pr_neon.Tpo .deps/rANS_static32x16pr_neon.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT tokenise_name3.lo -MD -MP -MF .deps/tokenise_name3.Tpo -c -o tokenise_name3.lo tokenise_name3.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT tokenise_name3.lo -MD -MP -MF .deps/tokenise_name3.Tpo -c tokenise_name3.c -fPIC -DPIC -o tokenise_name3.o mv -f .deps/tokenise_name3.Tpo .deps/tokenise_name3.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT arith_dynamic.lo -MD -MP -MF .deps/arith_dynamic.Tpo -c -o arith_dynamic.lo arith_dynamic.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT arith_dynamic.lo -MD -MP -MF .deps/arith_dynamic.Tpo -c arith_dynamic.c -fPIC -DPIC -o arith_dynamic.o mv -f .deps/arith_dynamic.Tpo .deps/arith_dynamic.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT htscodecs.lo -MD -MP -MF .deps/htscodecs.Tpo -c -o htscodecs.lo htscodecs.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT htscodecs.lo -MD -MP -MF .deps/htscodecs.Tpo -c htscodecs.c -fPIC -DPIC -o htscodecs.o mv -f .deps/htscodecs.Tpo .deps/htscodecs.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c -o utils.lo utils.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c utils.c -fPIC -DPIC -o utils.o mv -f .deps/utils.Tpo .deps/utils.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -msse4.1 -mssse3 -mpopcnt -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo -MD -MP -MF .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Tpo -c -o librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo `test -f 'rANS_static32x16pr_sse4.c' || echo './'`rANS_static32x16pr_sse4.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -msse4.1 -mssse3 -mpopcnt -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo -MD -MP -MF .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Tpo -c rANS_static32x16pr_sse4.c -fPIC -DPIC -o librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.o mv -f .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Tpo .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Plo /bin/sh ../libtool --tag=CC --mode=link /usr/local/libexec/ccache/cc -msse4.1 -mssse3 -mpopcnt -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o librANS_static32x16pr_sse4.la librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo -lthr -lbz2 -L/usr/local/lib libtool: link: ar cr .libs/librANS_static32x16pr_sse4.a librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.o libtool: link: ranlib .libs/librANS_static32x16pr_sse4.a libtool: link: ( cd ".libs" && rm -f "librANS_static32x16pr_sse4.la" && ln -s "../librANS_static32x16pr_sse4.la" "librANS_static32x16pr_sse4.la" ) /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo -MD -MP -MF .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Tpo -c -o librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo `test -f 'rANS_static32x16pr_avx2.c' || echo './'`rANS_static32x16pr_avx2.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo -MD -MP -MF .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Tpo -c rANS_static32x16pr_avx2.c -fPIC -DPIC -o librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.o mv -f .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Tpo .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Plo /bin/sh ../libtool --tag=CC --mode=link /usr/local/libexec/ccache/cc -mavx2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o librANS_static32x16pr_avx2.la librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo -lthr -lbz2 -L/usr/local/lib libtool: link: ar cr .libs/librANS_static32x16pr_avx2.a librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.o libtool: link: ranlib .libs/librANS_static32x16pr_avx2.a libtool: link: ( cd ".libs" && rm -f "librANS_static32x16pr_avx2.la" && ln -s "../librANS_static32x16pr_avx2.la" "librANS_static32x16pr_avx2.la" ) /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx512f -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo -MD -MP -MF .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Tpo -c -o librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo `test -f 'rANS_static32x16pr_avx512.c' || echo './'`rANS_static32x16pr_avx512.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx512f -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo -MD -MP -MF .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Tpo -c rANS_static32x16pr_avx512.c -fPIC -DPIC -o librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.o mv -f .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Tpo .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Plo /bin/sh ../libtool --tag=CC --mode=link /usr/local/libexec/ccache/cc -mavx512f -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o librANS_static32x16pr_avx512.la librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo -lthr -lbz2 -L/usr/local/lib libtool: link: ar cr .libs/librANS_static32x16pr_avx512.a librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.o libtool: link: ranlib .libs/librANS_static32x16pr_avx512.a libtool: link: ( cd ".libs" && rm -f "librANS_static32x16pr_avx512.la" && ln -s "../librANS_static32x16pr_avx512.la" "librANS_static32x16pr_avx512.la" ) /bin/sh ../libtool --tag=CC --mode=link /usr/local/libexec/ccache/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -version-info 3:2:1 -lpthread -fstack-protector-strong -o libhtscodecs.la -rpath /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib pack.lo rle.lo fqzcomp_qual.lo rANS_static.lo rANS_static4x16pr.lo rANS_static32x16pr.lo rANS_static32x16pr_neon.lo tokenise_name3.lo arith_dynamic.lo htscodecs.lo utils.lo librANS_static32x16pr_sse4.la librANS_static32x16pr_avx2.la librANS_static32x16pr_avx512.la -lm -lthr -lbz2 -L/usr/local/lib libtool: link: (cd .libs/libhtscodecs.lax/librANS_static32x16pr_sse4.a && ar x "/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/./.libs/librANS_static32x16pr_sse4.a") libtool: link: (cd .libs/libhtscodecs.lax/librANS_static32x16pr_avx2.a && ar x "/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/./.libs/librANS_static32x16pr_avx2.a") libtool: link: (cd .libs/libhtscodecs.lax/librANS_static32x16pr_avx512.a && ar x "/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/./.libs/librANS_static32x16pr_avx512.a") libtool: link: ar cr .libs/libhtscodecs.a pack.o rle.o fqzcomp_qual.o rANS_static.o rANS_static4x16pr.o rANS_static32x16pr.o rANS_static32x16pr_neon.o tokenise_name3.o arith_dynamic.o htscodecs.o utils.o .libs/libhtscodecs.lax/librANS_static32x16pr_sse4.a/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.o .libs/libhtscodecs.lax/librANS_static32x16pr_avx2.a/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.o .libs/libhtscodecs.lax/librANS_static32x16pr_avx512.a/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.o libtool: link: ranlib .libs/libhtscodecs.a libtool: link: rm -fr .libs/libhtscodecs.lax libtool: link: ( cd ".libs" && rm -f "libhtscodecs.la" && ln -s "../libhtscodecs.la" "libhtscodecs.la" ) gmake[8]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' Making all in . gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making all in tests gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static4x16pr_test.o -MD -MP -MF .deps/rANS_static4x16pr_test.Tpo -c -o rANS_static4x16pr_test.o rANS_static4x16pr_test.c mv -f .deps/rANS_static4x16pr_test.Tpo .deps/rANS_static4x16pr_test.Po /bin/sh ../libtool --tag=CC --mode=link /usr/local/libexec/ccache/cc -O2 -pipe -fstack-protector-strong 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.deps/libstaden_read_la-cram_stats.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c libtool: compile: /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -o libstaden_read_la-cram_io.o mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe 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libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz ../htscodecs/htscodecs/libhtscodecs.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: ar cr .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o 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libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o libtool: link: ranlib .libs/libstaden-read.a libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' Making all in progs gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT convert_trace.o -MD -MP -MF .deps/convert_trace.Tpo -c -o convert_trace.o convert_trace.c mv -f .deps/convert_trace.Tpo .deps/convert_trace.Po /bin/sh ../libtool --tag=CC --mode=link /usr/local/libexec/ccache/cc -O2 -pipe 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/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cram_size.o -MD -MP -MF .deps/cram_size.Tpo -c -o cram_size.o cram_size.c mv -f .deps/cram_size.Tpo .deps/cram_size.Po /bin/sh ../libtool --tag=CC --mode=link /usr/local/libexec/ccache/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/local/libexec/ccache/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_size cram_size.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cram_filter.o -MD -MP -MF .deps/cram_filter.Tpo -c -o cram_filter.o cram_filter.c mv -f .deps/cram_filter.Tpo .deps/cram_filter.Po /bin/sh ../libtool --tag=CC --mode=link /usr/local/libexec/ccache/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/local/libexec/ccache/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' Making all in tests gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' /usr/local/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cram_io_test.o -MD -MP -MF .deps/cram_io_test.Tpo -c -o cram_io_test.o cram_io_test.c mv -f .deps/cram_io_test.Tpo .deps/cram_io_test.Po /bin/sh ../libtool --tag=CC --mode=link /usr/local/libexec/ccache/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/local/libexec/ccache/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-build [ 6%] Performing install step for 'libstadenio' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && gmake install gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' Making install in htscodecs gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in htscodecs gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake install-am gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libhtscodecs.la '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' libtool: install: /usr/bin/install -c .libs/libhtscodecs.lai /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.la libtool: install: /usr/bin/install -c .libs/libhtscodecs.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a libtool: install: ranlib /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a gmake[7]: Nothing to be done for 'install-data-am'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' Making install in . gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[6]: Nothing to be done for 'install-exec-am'. mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/htscodecs' /usr/bin/install -c -m 644 htscodecs/arith_dynamic.h htscodecs/fqzcomp_qual.h htscodecs/rANS_static.h htscodecs/rANS_static4x16.h htscodecs/tokenise_name3.h htscodecs/pack.h htscodecs/rle.h htscodecs/varint.h htscodecs/htscodecs.h '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/htscodecs' gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in tests gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[6]: Nothing to be done for 'install-exec-am'. gmake[6]: Nothing to be done for 'install-data-am'. gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in io_lib gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.la libtool: install: /usr/bin/install -c .libs/libstaden-read.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a libtool: install: ranlib /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' Making install in progs gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' libtool: install: /usr/bin/install -c convert_trace /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/convert_trace libtool: install: /usr/bin/install -c makeSCF /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/makeSCF libtool: install: /usr/bin/install -c extract_seq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_seq libtool: install: /usr/bin/install -c extract_qual /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_qual libtool: install: /usr/bin/install -c extract_fastq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_fastq libtool: install: /usr/bin/install -c index_tar /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/index_tar libtool: install: /usr/bin/install -c scf_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_dump libtool: install: /usr/bin/install -c scf_info /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_info libtool: install: /usr/bin/install -c scf_update /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_update libtool: install: /usr/bin/install -c get_comment /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/get_comment libtool: install: /usr/bin/install -c hash_tar /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_tar libtool: install: /usr/bin/install -c hash_extract /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_extract libtool: install: /usr/bin/install -c hash_list /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_list libtool: install: /usr/bin/install -c trace_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/trace_dump libtool: install: /usr/bin/install -c hash_sff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_sff libtool: install: /usr/bin/install -c append_sff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/append_sff libtool: install: /usr/bin/install -c ztr_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/ztr_dump libtool: install: /usr/bin/install -c srf_dump_all /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_dump_all libtool: install: /usr/bin/install -c srf_index_hash /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_index_hash libtool: install: /usr/bin/install -c srf_extract_linear /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_extract_linear libtool: install: /usr/bin/install -c srf_extract_hash /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_extract_hash libtool: install: /usr/bin/install -c srf2fastq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf2fastq libtool: install: /usr/bin/install -c srf2fasta /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf2fasta libtool: install: /usr/bin/install -c srf_filter /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_filter libtool: install: /usr/bin/install -c srf_info /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_info libtool: install: /usr/bin/install -c srf_list /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_list libtool: install: /usr/bin/install -c hash_exp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_exp libtool: install: /usr/bin/install -c cram_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_dump libtool: install: /usr/bin/install -c cram_index /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_index libtool: install: /usr/bin/install -c scramble /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scramble libtool: install: /usr/bin/install -c scram_merge /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_merge libtool: install: /usr/bin/install -c scram_pileup /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_pileup libtool: install: /usr/bin/install -c scram_flagstat /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_flagstat libtool: install: /usr/bin/install -c scram_test /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_test libtool: install: /usr/bin/install -c cram_size /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_size libtool: install: /usr/bin/install -c cram_filter /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_filter gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' Making install in tests gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[5]: Nothing to be done for 'install-exec-am'. gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' /usr/bin/install -c io_lib-config '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man1' /usr/bin/install -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man1' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man3' /usr/bin/install -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man3' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man4' /usr/bin/install -c -m 644 man/man4/Read.4 '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man4' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/io_lib' /usr/bin/install -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h 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'libstadenio' /usr/local/bin/cmake -E make_directory /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles/libstadenio-complete /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-done gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 7%] Built target libstadenio /usr/local/bin/gmake -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 8%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem 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external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphdump && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/../common -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/. -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o -MF CMakeFiles/graphdump.dir/graphdump.cpp.o.d -o CMakeFiles/graphdump.dir/graphdump.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/graphdump.cpp [ 12%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphdump && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/../common -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/. -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -MF CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/common/dnachar.cpp [ 13%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphdump && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/../common -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/. -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/common/streamfastaparser.cpp [ 14%] Linking CXX static library libgraphdump.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphdump && /usr/local/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphdump && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libgraphdump.a CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o /usr/bin/llvm-ranlib libgraphdump.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 14%] Built target graphdump /usr/local/bin/gmake -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make 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external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -MF CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/common/dnachar.cpp [ 16%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing 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-fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp [ 17%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -MF CMakeFiles/twopaco.dir/compressedstring.cpp.o.d -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp [ 18%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/common/streamfastaparser.cpp [ 19%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/local/libexec/ccache/c++ 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-fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c [ 27%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 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-pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_gg2.c [ 31%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c [ 32%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 32%] Built target ksw2pp_basic /usr/local/bin/gmake -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 33%] Linking CXX static library libksw2pp.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 "/usr/bin/llvm-ar" qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o "/usr/bin/llvm-ranlib" libksw2pp.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 33%] Built target ksw2pp /usr/local/bin/gmake -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 34%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:27: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] 647 | mer_base_static(unsigned int k, const char* s) : super(k_) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:250:14: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 250 | auto c = seqVec[i]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:917:12: warning: variable 'totalKmersIshouldSee' set but not used [-Wunused-but-set-variable] 917 | size_t totalKmersIshouldSee{0} ; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:1074:11: warning: variable 'loopCounter' set but not used [-Wunused-but-set-variable] 1074 | int loopCounter = 0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>>, spp::sparsegroup>>, spp::libc_allocator>>>> *, std::pair>> *, std::input_iterator_tag, spp::libc_allocator>>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>>, spp::sparsegroup>>, spp::libc_allocator>>>> *, std::pair>> *, std::input_iterator_tag, spp::libc_allocator>>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::find_or_insert>>::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>>::operator[]' requested here 161 | path[ref_cnt].resize(contigCntPerPath); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:195:63: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 8, unsigned long, std::allocator, 64, false>::operator[]' requested here 195 | for (uint64_t i = 0; i < contigCntr; i++) edgeVec_[i] = 0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:310:24: note: in instantiation of member function 'compact::vector_imp::vector, 64, false>, unsigned long, 0, unsigned long, std::allocator, 64, false>::operator[]' requested here 310 | (*cpos_offsets)[0] = 0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::find_or_insert, unsigned int, VecHasher>::DefaultValue, std::vector &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:37: note: in instantiation of function template specialization 'spp::sparse_hash_map, unsigned int, VecHasher>::operator[] &>' requested here 414 | eqID = eqMap[tlist]; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:120:20: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 120 | return ((*rank_)[endPos] == 1); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:737:17: note: in instantiation of member function 'compact::vector_imp::vector, 64, true>, unsigned long, 0, unsigned long, std::allocator, 64, true>::operator[]' requested here 737 | posVec[idx] = kb1.pos(); | ^ 22 warnings generated. [ 35%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp:13: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp:26:19: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 26 | auto spos = underlying().contigOffsets_[contigRank]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cpp:343:17: note: in instantiation of member function 'PufferfishBaseIndex::contigRange' requested here 343 | template class PufferfishBaseIndex; | ^ 13 warnings generated. [ 35%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:13: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] 647 | mer_base_static(unsigned int k, const char* s) : super(k_) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp:26:19: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 26 | auto spos = underlying().contigOffsets_[contigRank]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:207:30: note: in instantiation of member function 'PufferfishBaseIndex::contigRange' requested here 207 | auto contigIterRange = contigRange(rank); | ^ 14 warnings generated. [ 36%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishSparseIndex.hpp:12: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishSparseIndex.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishSparseIndex.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:438:23: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 438 | auto sampledPos = sampledPos_[currRank]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:384:9: warning: variable 'inLoop' set but not used [-Wunused-but-set-variable] 384 | int inLoop = 0; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:480:9: warning: variable 'inLoop' set but not used [-Wunused-but-set-variable] 480 | int inLoop = 0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishSparseIndex.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:379:19: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 379 | if (presenceVec_[idx] == 1) { | ^ 16 warnings generated. [ 37%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishLossyIndex.hpp:11: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishLossyIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishLossyIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:159:39: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 159 | if (res < numKmers_ and presenceVec_[res] == 1) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishLossyIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:162:22: note: in instantiation of member function 'compact::vector_imp::vector, 64, false>, unsigned long, 0, unsigned long, std::allocator, 64, false>::operator[]' requested here 162 | pos = sampledPos_[currRank]; | ^ 14 warnings generated. [ 38%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o -MF CMakeFiles/puffer.dir/edlib.cpp.o.d -o CMakeFiles/puffer.dir/edlib.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/edlib.cpp [ 39%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o -MF CMakeFiles/puffer.dir/Util.cpp.o.d -o CMakeFiles/puffer.dir/Util.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:216:51: warning: 'const' qualifier on reference type 'decltype(* jointMemsList.begin())' (aka 'pufferfish::util::JointMems &') has no effect [-Wignored-reference-qualifiers] 216 | [best_pair_in_target, thresh](const decltype(*jointMemsList.begin())& jm) -> bool { | ^~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:239:61: warning: lambda capture 'coverageRatio' is not required to be captured for this use [-Wunused-lambda-capture] 239 | auto orphanFiller = [&jointMemsList, &maxCoverage, &coverageRatio, &maxLeftOrRight, &leftOrphan, &rightOrphan, thresh, ithresh, orphan_chain_sub_thresh] | ~~~^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:239:120: warning: lambda capture 'thresh' is not required to be captured for this use [-Wunused-lambda-capture] 239 | auto orphanFiller = [&jointMemsList, &maxCoverage, &coverageRatio, &maxLeftOrRight, &leftOrphan, &rightOrphan, thresh, ithresh, orphan_chain_sub_thresh] | ~~^~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:239:128: warning: lambda capture 'ithresh' is not used [-Wunused-lambda-capture] 239 | auto orphanFiller = [&jointMemsList, &maxCoverage, &coverageRatio, &maxLeftOrRight, &leftOrphan, &rightOrphan, thresh, ithresh, orphan_chain_sub_thresh] | ~~^~~~~~~ 15 warnings generated. [ 40%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o -MF CMakeFiles/puffer.dir/rank9sel.cpp.o.d -o CMakeFiles/puffer.dir/rank9sel.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9sel.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9sel.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/rank9sel.hpp:27: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ 7 warnings generated. [ 40%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o -MF CMakeFiles/puffer.dir/rank9b.cpp.o.d -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9b.cpp [ 41%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -MF CMakeFiles/puffer.dir/PufferfishValidate.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:16: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] 647 | mer_base_static(unsigned int k, const char* s) : super(k_) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:154:35: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 2, unsigned long, std::allocator, 64, false>::operator[]' requested here 154 | kb.shiftFw(static_cast(refSeq[gpos])); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:479:14: note: in instantiation of function template specialization 'doPufferfishInternalValidate' requested here 479 | return doPufferfishInternalValidate(pi, validateOpts); | ^ 14 warnings generated. [ 42%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o -MF CMakeFiles/puffer.dir/PufferfishStats.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishStats.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:16: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:16: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:17: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] 647 | mer_base_static(unsigned int k, const char* s) : super(k_) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:16: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:53:24: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 53 | if (not visited[v]) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:16: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:141:162: note: in instantiation of member function 'compact::vector_imp::vector, 64, false>, unsigned long, 0, unsigned long, std::allocator, 64, false>::operator[]' requested here 141 | << " contigOffsets size: " << contigOffsets_.size() << ", bpe: " << bits_per_element << " , total elements in the contig table: " << contigOffsets_[contigOffsets_.size()-1] << "\n"; | ^ 15 warnings generated. [ 43%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -MF CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp:15: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] 647 | mer_base_static(unsigned int k, const char* s) : super(k_) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp:25:78: warning: unused parameter 'k' [-Wunused-parameter] 25 | std::vector get_kmers(const std::string& fasta_file, uint32_t k) { | ^ 14 warnings generated. [ 44%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -MF CMakeFiles/puffer.dir/PufferfishExamine.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishExamine.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishExamine.cpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishExamine.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PuffAligner.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishExamine.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ 12 warnings generated. [ 44%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -MF CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp:17: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/SAMWriter.hpp:4: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BinWriter.hpp:31:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 31 | BinWriter(std::vector&& bin_data) :_bin_data(move(bin_data)) {}; | ^ | std:: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp:44:12: warning: variable 'rn' set but not used [-Wunused-but-set-variable] 44 | size_t rn{0}; | ^ 14 warnings generated. [ 45%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o -MF CMakeFiles/puffer.dir/FastxParser.cpp.o.d -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FastxParser.cpp [ 46%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:109:15: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 2, unsigned long, std::allocator, 64, false>::operator[]' requested here 109 | seqVec[offset + i] = c; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>>, spp::sparsegroup>>, spp::libc_allocator>>>> *, std::pair>> *, std::input_iterator_tag, spp::libc_allocator>>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>>, spp::sparsegroup>>, spp::libc_allocator>>>> *, std::pair>> *, std::input_iterator_tag, spp::libc_allocator>>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::find_or_insert>>::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>>::operator[]' requested here 161 | path[ref_cnt].resize(contigCntPerPath); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:195:63: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 8, unsigned long, std::allocator, 64, false>::operator[]' requested here 195 | for (uint64_t i = 0; i < contigCntr; i++) edgeVec_[i] = 0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:310:24: note: in instantiation of member function 'compact::vector_imp::vector, 64, false>, unsigned long, 0, unsigned long, std::allocator, 64, false>::operator[]' requested here 310 | (*cpos_offsets)[0] = 0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::find_or_insert, unsigned int, VecHasher>::DefaultValue, std::vector &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:37: note: in instantiation of function template specialization 'spp::sparse_hash_map, unsigned int, VecHasher>::operator[] &>' requested here 414 | eqID = eqMap[tlist]; | ^ 16 warnings generated. [ 47%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o -MF CMakeFiles/puffer.dir/PufferFS.cpp.o.d -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferFS.cpp [ 48%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/cc -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -MF CMakeFiles/puffer.dir/xxhash.c.o.d -o CMakeFiles/puffer.dir/xxhash.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/xxhash.c [ 49%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -MF CMakeFiles/puffer.dir/FixFasta.cpp.o.d -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:2: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] 647 | mer_base_static(unsigned int k, const char* s) : super(k_) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:3: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/clipp.h:1409:13: warning: variable 'i' set but not used [-Wunused-but-set-variable] 1409 | int i = 0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:27: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/digestpp/digestpp.hpp:5: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/digestpp/hasher.hpp:136:10: warning: variable 'len' set but not used [-Wunused-but-set-variable] 136 | size_t len = 0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:27: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/digestpp/digestpp.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/digestpp/algorithm/k12m14.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/digestpp/algorithm/detail/k12m14_provider.hpp:86:77: warning: unused parameter 'reallen' [-Wunused-parameter] 86 | inline void transform(const unsigned char* data, uint64_t num_blks, size_t reallen) | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:4: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned long, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned long, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned long, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned long, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:264:33: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 264 | duplicateNames[dupInfo.txId].push_back(processedName); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:4: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, std::string *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, std::string *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:490:20: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 490 | auto it = dset.insert(dname); | ^ 6 warnings generated. [ 49%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -MF CMakeFiles/puffer.dir/MemCollector.cpp.o.d -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemCollector.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemCollector.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemCollector.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemCollector.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemCollector.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemCollector.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemCollector.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ 12 warnings generated. [ 50%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemChainer.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemChainer.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemChainer.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemChainer.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemChainer.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemChainer.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemChainer.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemChainer.cpp:95:16: warning: variable 'mappings' set but not used [-Wunused-but-set-variable] 95 | uint32_t mappings{0}; | ^ 13 warnings generated. [ 51%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -MF CMakeFiles/puffer.dir/PuffAligner.cpp.o.d -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PuffAligner.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PuffAligner.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PuffAligner.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PuffAligner.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PuffAligner.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PuffAligner.cpp:2: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PuffAligner.hpp:102:12: warning: private field 'k' is not used [-Wunused-private-field] 102 | uint32_t k; | ^ 12 warnings generated. [ 52%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -MF CMakeFiles/puffer.dir/PufferfishAligner.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:45: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/SelectiveAlignmentUtils.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PuffAligner.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:48: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:56: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/SAMWriter.hpp:4: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BinWriter.hpp:31:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 31 | BinWriter(std::vector&& bin_data) :_bin_data(move(bin_data)) {}; | ^ | std:: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 252 | : std::integral_constant>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:1022:31: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 1022 | gene_names.insert(processedName); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant>' requested here 254 | is_trivially_destructible::value> {}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:1818:32: note: in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:1022:31: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 1022 | gene_names.insert(processedName); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:259:17: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:1819:22: note: in instantiation of template class 'phmap::is_trivially_copy_assignable>' requested here 1819 | phmap::is_trivially_copy_assignable>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:1022:31: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 1022 | gene_names.insert(processedName); | ^ 16 warnings generated. [ 53%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/RefSeqConstructor.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/RefSeqConstructor.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/RefSeqConstructor.hpp:5: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:143:47: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/RefSeqConstructor.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:338:23: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 8, unsigned long, std::allocator, 64, false>::operator[]' requested here 338 | uint8_t edgeVec = edges[contig.contigIdx_] ; | ^ 14 warnings generated. [ 54%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/metro/metrohash64.cpp [ 54%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -MF CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o.d -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/LibraryFormat.cpp [ 55%] Linking CXX static library libpuffer.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o /usr/bin/llvm-ranlib libpuffer.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 55%] Built target puffer /usr/local/bin/gmake -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/src /wrkdirs/usr/ports/biology/salmon/work/.build/src/CMakeFiles/salmon_core.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 55%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -MF CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o.d -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/jellyfish/mer_dna.cc In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/jellyfish/mer_dna.cc:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hpp:35: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:117:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 117 | __int128_ns::__print(os, x); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 102 | char padding[nb_padding]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:123:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 123 | __int128_ns::__print(os, x); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 102 | char padding[nb_padding]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ 3 warnings generated. [ 56%] Building CXX object src/CMakeFiles/salmon_core.dir/backtrace.cc.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/backtrace.cc.o -MF CMakeFiles/salmon_core.dir/backtrace.cc.o.d -o CMakeFiles/salmon_core.dir/backtrace.cc.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/backtrace.cc [ 57%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/xxhash.c.o -MF CMakeFiles/salmon_core.dir/xxhash.c.o.d -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/xxhash.c cc: warning: argument unused during compilation: '-stdlib=libc++' [-Wunused-command-line-argument] [ 58%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -MF CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o.d -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/TranscriptGroup.cpp [ 59%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -MF CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o.d -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EffectiveLengthStats.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EffectiveLengthStats.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EffectiveLengthStats.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:501:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 501 | return setConstant(Scalar(0)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EffectiveLengthStats.cpp:38:7: note: in instantiation of member function 'Eigen::DenseBase>::setZero' requested here 38 | eel.setZero(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EffectiveLengthStats.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EffectiveLengthStats.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EffectiveLengthStats.cpp:42:10: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 42 | return eel; | ^ 2 warnings generated. [ 60%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -MF CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o.d -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/LibraryFormat.cpp [ 60%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -MF CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o.d -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GenomicFeature.cpp [ 61%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -MF CMakeFiles/salmon_core.dir/VersionChecker.cpp.o.d -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/VersionChecker.cpp [ 62%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SBModel.cpp.o -MF CMakeFiles/salmon_core.dir/SBModel.cpp.o.d -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hpp:35: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:117:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 117 | __int128_ns::__print(os, x); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 102 | char padding[nb_padding]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:123:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 123 | __int128_ns::__print(os, x); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 102 | char padding[nb_padding]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:501:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 501 | return setConstant(Scalar(0)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:47:14: note: in instantiation of member function 'Eigen::DenseBase>::setZero' requested here 47 | _marginals.setZero(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>>, Eigen::internal::evaluator, Eigen::Array>>, Eigen::internal::add_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>>, Eigen::internal::evaluator, Eigen::Array>>, Eigen::internal::add_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop>, Eigen::CwiseNullaryOp, Eigen::Array>, Eigen::internal::add_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment>, Eigen::CwiseNullaryOp, Eigen::Array>, Eigen::internal::add_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias>, Eigen::CwiseNullaryOp, Eigen::Array>, Eigen::internal::add_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:29:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment>, Eigen::CwiseNullaryOp, Eigen::Array>, Eigen::internal::add_assign_op>' requested here 29 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::add_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:48:22: note: in instantiation of member function 'Eigen::ArrayBase>>::operator+=' requested here 48 | _marginals.array() += _prior_prob; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, -1, 1, true>, -1, 1>>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::div_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1, true>, -1, 1>>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::div_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, -1, 1, true>, -1, 1>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, -1, 1, true>, -1, 1>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, -1, 1, true>, -1, 1>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:45:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, -1, 1, true>, -1, 1>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 45 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::div_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:237:55: note: in instantiation of member function 'Eigen::DenseBase, -1, 1, true>, -1, 1>>::operator/=' requested here 237 | _probs.col(pos).segment(nodeStart, rowsPerNode) /= tot; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, -1, 1, true>>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::div_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1, true>>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::div_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, -1, 1, true>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, -1, 1, true>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, -1, 1, true>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:45:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, -1, 1, true>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 45 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::div_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:245:25: note: in instantiation of member function 'Eigen::DenseBase, -1, 1, true>>::operator/=' requested here 245 | _marginals.col(pos) /= numStates; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseUnaryOp<(lambda at /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:251:18), const Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseUnaryOp<(lambda at /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:251:18), const Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseUnaryOp<(lambda at /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:251:18), const Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseUnaryOp<(lambda at /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:251:18), const Eigen::Matrix>, Eigen::internal::assign_op>' requested here 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseUnaryOp<(lambda at /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:251:18), const Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:254:10: note: in instantiation of function template specialization 'Eigen::Matrix::operator=>>' requested here 254 | _probs = _probs.unaryExpr(takeLog); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::add_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::add_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::add_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::add_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::add_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:177:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::Matrix, Eigen::internal::add_assign_op>' requested here 177 | call_assignment(derived(), other.derived(), internal::add_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:288:60: note: in instantiation of function template specialization 'Eigen::MatrixBase>::operator+=>' requested here 288 | void SBModel::combineCounts(const SBModel& other) { _probs += other._probs; } | ^ 13 warnings generated. [ 63%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o -MF CMakeFiles/salmon_core.dir/FastxParser.cpp.o.d -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FastxParser.cpp [ 64%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -MF CMakeFiles/salmon_core.dir/StadenUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/StadenUtils.cpp [ 64%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.hpp:145: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.tpp:609:12: warning: variable 'n' set but not used [-Wunused-but-set-variable] 609 | size_t n{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 252 | : std::integral_constant>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant>' requested here 254 | is_trivially_destructible::value> {}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1818:32: note: in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:259:17: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1819:22: note: in instantiation of template class 'phmap::is_trivially_copy_assignable>' requested here 1819 | phmap::is_trivially_copy_assignable>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:375:10: warning: variable 'clusterID' set but not used [-Wunused-but-set-variable] 375 | size_t clusterID = 0; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:472:10: warning: variable 'clusterID' set but not used [-Wunused-but-set-variable] 472 | size_t clusterID = 0; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3210:34: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 3210 | geneExps[gn].push_back(move(er)); | ^ | std:: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:501:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 501 | return setConstant(Scalar(0)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:2717:27: note: in instantiation of member function 'Eigen::DenseBase>::setZero' requested here 2717 | contextCountsFP.setZero(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, -1, -1, true>>, Eigen::internal::evaluator, -1, -1, true>>>, Eigen::internal::swap_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Swap.h:20:11: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, -1, true>>, Eigen::internal::evaluator, -1, -1, true>>>, Eigen::internal::swap_assign_op, 1>' requested here 20 | : public generic_dense_assignment_kernel, BuiltIn> | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, -1, true>>, Eigen::internal::evaluator, -1, -1, true>>>, Eigen::internal::swap_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, -1, -1, true>, Eigen::Reverse, -1, -1, true>>, Eigen::internal::swap_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, -1, -1, true>, Eigen::Reverse, -1, -1, true>>, Eigen::internal::swap_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, -1, -1, true>, Eigen::Reverse, -1, -1, true>>, Eigen::internal::swap_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:418:7: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, -1, -1, true>, Eigen::Reverse, -1, -1, true>>, Eigen::internal::swap_assign_op>' requested here 418 | call_assignment(derived(), other.const_cast_derived(), internal::swap_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Reverse.h:144:20: note: in instantiation of function template specialization 'Eigen::DenseBase, -1, -1, true>>::swap, -1, -1, true>>>' requested here 144 | leftCols(half).swap(rightCols(half).reverse()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3048:28: note: in instantiation of member function 'Eigen::DenseBase>::reverseInPlace' requested here 3048 | seqFactorsRC.reverseInPlace(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, -1, 1, true>, -1, 1>>, Eigen::internal::evaluator, -1, 1, true>, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Swap.h:20:11: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1, true>, -1, 1>>, Eigen::internal::evaluator, -1, 1, true>, -1, 1>>>, Eigen::internal::swap_assign_op, 1>' requested here 20 | : public generic_dense_assignment_kernel, BuiltIn> | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1, true>, -1, 1>>, Eigen::internal::evaluator, -1, 1, true>, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, -1, 1, true>, -1, 1>, Eigen::Reverse, -1, 1, true>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, -1, 1, true>, -1, 1>, Eigen::Reverse, -1, 1, true>, -1, 1>>, Eigen::internal::swap_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, -1, 1, true>, -1, 1>, Eigen::Reverse, -1, 1, true>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:418:7: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, -1, 1, true>, -1, 1>, Eigen::Reverse, -1, 1, true>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 418 | call_assignment(derived(), other.const_cast_derived(), internal::swap_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Reverse.h:148:29: note: in instantiation of function template specialization 'Eigen::DenseBase, -1, 1, true>, -1, 1>>::swap, -1, 1, true>, -1, 1>>>' requested here 148 | col(half).head(half2).swap(col(half).tail(half2).reverse()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3048:28: note: in instantiation of member function 'Eigen::DenseBase>::reverseInPlace' requested here 3048 | seqFactorsRC.reverseInPlace(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, -1, 1>>, Eigen::internal::evaluator, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Swap.h:20:11: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1>>, Eigen::internal::evaluator, -1, 1>>>, Eigen::internal::swap_assign_op, 1>' requested here 20 | : public generic_dense_assignment_kernel, BuiltIn> | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1>>, Eigen::internal::evaluator, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, -1, 1>, Eigen::Reverse, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, -1, 1>, Eigen::Reverse, -1, 1>>, Eigen::internal::swap_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, -1, 1>, Eigen::Reverse, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:418:7: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, -1, 1>, Eigen::Reverse, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 418 | call_assignment(derived(), other.const_cast_derived(), internal::swap_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Reverse.h:154:19: note: in instantiation of function template specialization 'Eigen::DenseBase, -1, 1>>::swap, -1, 1>>>' requested here 154 | topRows(half).swap(bottomRows(half).reverse()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3048:28: note: in instantiation of member function 'Eigen::DenseBase>::reverseInPlace' requested here 3048 | seqFactorsRC.reverseInPlace(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, 1, 1>, -1, 1>>, Eigen::internal::evaluator, 1, 1>, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Swap.h:20:11: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, 1, 1>, -1, 1>>, Eigen::internal::evaluator, 1, 1>, -1, 1>>>, Eigen::internal::swap_assign_op, 1>' requested here 20 | : public generic_dense_assignment_kernel, BuiltIn> | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, 1, 1>, -1, 1>>, Eigen::internal::evaluator, 1, 1>, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, 1, 1>, -1, 1>, Eigen::Reverse, 1, 1>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, 1, 1>, -1, 1>, Eigen::Reverse, 1, 1>, -1, 1>>, Eigen::internal::swap_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, 1, 1>, -1, 1>, Eigen::Reverse, 1, 1>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:418:7: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, 1, 1>, -1, 1>, Eigen::Reverse, 1, 1>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 418 | call_assignment(derived(), other.const_cast_derived(), internal::swap_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Reverse.h:158:29: note: in instantiation of function template specialization 'Eigen::DenseBase, 1, 1>, -1, 1>>::swap, 1, 1>, -1, 1>>>' requested here 158 | row(half).head(half2).swap(row(half).tail(half2).reverse()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3048:28: note: in instantiation of member function 'Eigen::DenseBase>::reverseInPlace' requested here 3048 | seqFactorsRC.reverseInPlace(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3158:10: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 3158 | return effLensOut; | ^ 21 warnings generated. [ 65%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -MF CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DistributionUtils.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DistributionUtils.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DistributionUtils.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DistributionUtils.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DistributionUtils.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ 7 warnings generated. [ 66%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonExceptions.cpp [ 67%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonStringUtils.cpp [ 68%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -MF CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o.d -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SimplePosBias.cpp [ 69%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type 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-I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -MF CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o.d -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/src/pufferfish/metro/metrohash64.cpp [ 70%] Linking CXX static library libsalmon_core.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 "/usr/bin/llvm-ar" qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/backtrace.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o "/usr/bin/llvm-ranlib" libsalmon_core.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 70%] Built target salmon_core /usr/local/bin/gmake -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -MF CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o.d -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinUtils.cpp In file included from 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[ 73%] Linking CXX static library libalevin_core.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 "/usr/bin/llvm-ar" qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o "/usr/bin/llvm-ranlib" libalevin_core.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 73%] Built target alevin_core /usr/local/bin/gmake -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 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-DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -pthread -MD -MT src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ 4 warnings generated. [ 76%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -pthread -MD -MT src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -MF CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o.d -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/src/pufferfish/rank9b.cpp [ 77%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -pthread -MD -MT src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/GCSampleTests.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/GCSampleTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/GCSampleTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/GCSampleTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/GCSampleTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ 7 warnings generated. [ 78%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -pthread -MD -MT src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/LibraryTypeTests.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/LibraryTypeTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/LibraryTypeTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/LibraryTypeTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/LibraryTypeTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ 7 warnings generated. [ 79%] Linking CXX executable unitTests cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/unitTests.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -lpthread -fstack-protector-strong -Xlinker --dependency-file=CMakeFiles/unitTests.dir/link.d CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -o unitTests -L/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/lib -L/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib -L/usr/local/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib:/usr/local/lib" /usr/local/lib/libboost_iostreams.a /usr/local/lib/libboost_system.a /usr/local/lib/libboost_filesystem.a /usr/local/lib/libboost_timer.a /usr/local/lib/libboost_chrono.a /usr/local/lib/libboost_program_options.a /usr/local/lib/libboost_regex.a libsalmon_core.a libalevin_core.a -lgff libUnitTestsMain.a /usr/local/lib/libboost_iostreams.a /usr/local/lib/libboost_system.a /usr/local/lib/libboost_filesystem.a /usr/local/lib/libboost_timer.a /usr/local/lib/libboost_chrono.a /usr/local/lib/libboost_program_options.a /usr/local/lib/libboost_regex.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a /usr/local/lib/libcurl.a /usr/lib/libz.a -lm /usr/lib/liblzma.a /usr/lib/libmd.a /usr/lib/libbz2.a /usr/local/lib/libtbb.so.12.15 /usr/local/lib/libtbbmalloc.so.2.15 -lgomp -lrt -lgff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a /usr/local/lib/libcurl.a /usr/lib/libz.a -lm /usr/lib/liblzma.a /usr/lib/libmd.a /usr/lib/libbz2.a -lgomp -lrt Copying unitTests cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E copy /wrkdirs/usr/ports/biology/salmon/work/.build/src/unitTests /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/unitTests gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 79%] Built target unitTests /usr/local/bin/gmake -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/src /wrkdirs/usr/ports/biology/salmon/work/.build/src/CMakeFiles/salmon.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 80%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/EMUtils.cpp.o -MF CMakeFiles/salmon.dir/EMUtils.cpp.o.d -o CMakeFiles/salmon.dir/EMUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ 19 warnings generated. [ 81%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -MF CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.hpp:145: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.tpp:609:12: warning: variable 'n' set but not used [-Wunused-but-set-variable] 609 | size_t n{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 252 | : std::integral_constant>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant>' requested here 254 | is_trivially_destructible::value> {}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1818:32: note: in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:259:17: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1819:22: note: in instantiation of template class 'phmap::is_trivially_copy_assignable>' requested here 1819 | phmap::is_trivially_copy_assignable>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedEMOptimizer.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:450:12: warning: variable 'totalLen' set but not used [-Wunused-but-set-variable] 450 | double totalLen{0.0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:603:10: warning: variable 'totalLen' set but not used [-Wunused-but-set-variable] 603 | double totalLen{0.0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:776:10: warning: variable 'totalLen' set but not used [-Wunused-but-set-variable] 776 | double totalLen{0.0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:281:17: warning: lambda capture 'alphaIn' is not used [-Wunused-lambda-capture] 281 | [&eqVec, &alphaIn, &alphaOut, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:278:20: note: while substituting into a lambda expression here 278 | arena.execute([&]{ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:939:7: note: in instantiation of function template specialization 'VBEMUpdate_>>' requested here 939 | VBEMUpdate_(arena, eqVec, priorAlphas, alphas, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:189:17: warning: lambda capture 'priorAlphas' is not used [-Wunused-lambda-capture] 189 | [&eqVec, &priorAlphas, &alphaIn, &alphaOut](const BlockedIndexRange& range) -> void { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:186:20: note: while substituting into a lambda expression here 186 | arena.execute([&]{ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:950:7: note: in instantiation of function template specialization 'EMUpdate_>>' requested here 950 | EMUpdate_(arena, eqVec, priorAlphas, alphas, alphasPrime); | ^ 33 warnings generated. [ 82%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -MF CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:17: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:368:16: warning: variable 'muSum' set but not used [-Wunused-but-set-variable] 368 | double muSum{0.0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:247:12: warning: variable 'totalNumFrags' set but not used [-Wunused-but-set-variable] 247 | uint32_t totalNumFrags = 0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, const unsigned short &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:747:36: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 747 | arboFragCounts[gid][it.first] += it.second; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned long *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned long *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3226:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3226 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4219:56: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4219 | std::pair p = rep.insert(obj); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:971:16: note: in instantiation of member function 'spp::sparse_hash_set::insert' requested here 971 | umis.insert( it.first ); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, std::string &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:1087:40: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GZipWriter.hpp:17: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:40: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_map.h:34: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h:377:42: warning: inline function 'tsl::detail_array_hash::array_bucket, unsigned short, true>::append' is not defined [-Wundefined-inline] 377 | const_iterator __attribute__((used)) append(const_iterator end_of_bucket, const CharT* key, size_type key_size, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h:1318:74: note: used here 1318 | std::pair emplace_impl(std::size_t ibucket, typename array_bucket::const_iterator end_of_bucket, | ^ 32 warnings generated. [ 82%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -MF CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:28: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.hpp:145: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.tpp:609:12: warning: variable 'n' set but not used [-Wunused-but-set-variable] 609 | size_t n{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 252 | : std::integral_constant>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant>' requested here 254 | is_trivially_destructible::value> {}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1818:32: note: in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:259:17: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1819:22: note: in instantiation of template class 'phmap::is_trivially_copy_assignable>' requested here 1819 | phmap::is_trivially_copy_assignable>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:217:22: warning: variable 'muSum' set but not used [-Wunused-but-set-variable] 217 | double muSum = 0.0; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:502:14: warning: variable 'asum' set but not used [-Wunused-but-set-variable] 502 | double asum = {0.0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:27: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:27: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:27: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:27: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:27: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:27: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:129:13: warning: lambda capture 'beta' is not used [-Wunused-lambda-capture] 129 | [&, beta](const BlockedIndexRange& range) -> void { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:124:22: note: while substituting into a lambda expression here 124 | arena.execute([&]{ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:476:7: note: in instantiation of function template specialization 'sampleRoundNonCollapsedMultithreaded_>>' requested here 476 | sampleRoundNonCollapsedMultithreaded_( | ^ 31 warnings generated. [ 83%] Building CXX object src/CMakeFiles/salmon.dir/Salmon.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/Salmon.cpp.o -MF CMakeFiles/salmon.dir/Salmon.cpp.o.d -o CMakeFiles/salmon.dir/Salmon.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Salmon.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Salmon.cpp:49: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Salmon.cpp:49: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Salmon.cpp:49: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Salmon.cpp:49: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ 13 warnings generated. [ 84%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -MF CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o.d -o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ 20 warnings generated. [ 85%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/Graph.cpp.o -MF CMakeFiles/salmon.dir/Graph.cpp.o.d -o CMakeFiles/salmon.dir/Graph.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:40: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::find_or_insert, unsigned int, boost::hash>>::DefaultValue, std::pair &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp:10:24: note: in instantiation of function template specialization 'spp::sparse_hash_map, unsigned int, boost::hash>>::operator[] &>' requested here 10 | index = vertMap[node]; | ^ 17 warnings generated. [ 86%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/DedupUMI.cpp.o -MF CMakeFiles/salmon.dir/DedupUMI.cpp.o.d -o CMakeFiles/salmon.dir/DedupUMI.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:40: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GZipWriter.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:394:18: warning: variable 'readspmol' set but not used [-Wunused-but-set-variable] 394 | uint16_t readspmol {0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:32:13: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 32 | tidMap[txp].emplace_back(eqId); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2680:30: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested here 2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2846:13: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_maybe_shrink' requested here 2846 | _maybe_shrink(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3799:45: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::resize' requested here 3799 | void resize(size_type cnt) { rep.resize(cnt); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3801:41: note: in instantiation of member function 'spp::sparse_hash_map, unsigned int, boost::hash>>::resize' requested here 3801 | void reserve(size_type cnt) { resize(cnt); } // c++11 | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:39:18: note: in instantiation of member function 'spp::sparse_hash_map, unsigned int, boost::hash>>::reserve' requested here 39 | vertexIndexMap.reserve(numClasses); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, std::pair>>, spp::sparsegroup, std::pair>>, spp::libc_allocator, std::pair>>>> *, std::pair, std::pair>> *, std::input_iterator_tag, spp::libc_allocator, std::pair>>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, std::pair>>, spp::sparsegroup, std::pair>>, spp::libc_allocator, std::pair>>>> *, std::pair, std::pair>> *, std::input_iterator_tag, spp::libc_allocator, std::pair>>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, std::pair>>, std::vector, boost::hash>, spp::sparse_hash_map, std::pair>, boost::hash>>::SelectKey, spp::sparse_hash_map, std::pair>, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, std::pair>>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, std::pair>>, std::vector, boost::hash>, spp::sparse_hash_map, std::pair>, boost::hash>>::SelectKey, spp::sparse_hash_map, std::pair>, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, std::pair>>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, std::pair>>, std::vector, boost::hash>, spp::sparse_hash_map, std::pair>, boost::hash>>::SelectKey, spp::sparse_hash_map, std::pair>, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, std::pair>>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, std::pair>>, std::vector, boost::hash>, spp::sparse_hash_map, std::pair>, boost::hash>>::SelectKey, spp::sparse_hash_map, std::pair>, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, std::pair>>>>::find_or_insert, std::pair>, boost::hash>>::DefaultValue, std::vector &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:285:20: note: in instantiation of function template specialization 'spp::sparse_hash_map, std::pair>, boost::hash>>::operator[] &>' requested here 285 | eqclassHash[genesVec].first += 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned short &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:286:37: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 286 | eqclassHash[genesVec].second[readspmol] += 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int>, std::vector, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::find_or_insert, unsigned int, boost::hash>>::DefaultValue, std::vector &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:413:20: note: in instantiation of function template specialization 'spp::sparse_hash_map, unsigned int, boost::hash>>::operator[] &>' requested here 413 | eqclassHash[genesVec] += 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:477:24: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 477 | vertexIndices[gene] = gid; | ^ 33 warnings generated. [ 87%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/Alevin.cpp.o -MF CMakeFiles/salmon.dir/Alevin.cpp.o.d -o CMakeFiles/salmon.dir/Alevin.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:40: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GZipWriter.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:60: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeModel.hpp:168:31: warning: loop variable 'trueBarcode' creates a copy from type 'const std::string' (aka 'const basic_string') [-Wrange-loop-construct] 168 | for(const std::string trueBarcode: trueBarcodes){ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeModel.hpp:168:13: note: use reference type 'const std::string &' (aka 'const basic_string &') to prevent copying 168 | for(const std::string trueBarcode: trueBarcodes){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | & /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const value_type' (aka 'const std::string') [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:488:8: note: use reference type 'const value_type &' (aka 'const std::string &') to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~~~~~~~~~~~~~ | & In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:58: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:40: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_map.h:34: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h:377:42: warning: inline function 'tsl::detail_array_hash::array_bucket, unsigned short, true>::append' is not defined [-Wundefined-inline] 377 | const_iterator __attribute__((used)) append(const_iterator end_of_bucket, const CharT* key, size_type key_size, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h:1318:74: note: used here 1318 | std::pair emplace_impl(std::size_t ibucket, typename array_bucket::const_iterator end_of_bucket, | ^ 29 warnings generated. [ 87%] Building CXX object src/CMakeFiles/salmon.dir/AlevinHash.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/AlevinHash.cpp.o -MF CMakeFiles/salmon.dir/AlevinHash.cpp.o.d -o CMakeFiles/salmon.dir/AlevinHash.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:40: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GZipWriter.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, std::string &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:12:14: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 12 | txpIdxMap[ transcripts[i] ] = i; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:35:19: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 35 | txpToGeneMap[tid] = gid; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:98:19: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 98 | barcodeMap[i] = i; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, const std::string &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:105:23: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 105 | trueBarcodeMap[bc] = idx; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:40: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_map.h:34: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h:377:42: warning: inline function 'tsl::detail_array_hash::array_bucket, unsigned short, true>::append' is not defined [-Wundefined-inline] 377 | const_iterator __attribute__((used)) append(const_iterator end_of_bucket, const CharT* key, size_type key_size, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h:1318:74: note: used here 1318 | std::pair emplace_impl(std::size_t ibucket, typename array_bucket::const_iterator end_of_bucket, | ^ 31 warnings generated. [ 88%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -MF CMakeFiles/salmon.dir/SalmonAlevin.cpp.o.d -o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:90: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/radicl/BasicBinWriter.hpp:22:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 22 | BasicBinWriter(std::vector&& bin_data) : _bin_data(move(bin_data)){}; | ^ | std:: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:97: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:117: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:16:3: warning: explicitly defaulted move constructor is implicitly deleted [-Wdefaulted-function-deleted] 16 | ForgettingMassCalculator(ForgettingMassCalculator&&) = default; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:141:14: note: move constructor of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move constructor 141 | std::mutex ffMutex_; | ^ /usr/include/c++/v1/__mutex/mutex.h:30:3: note: 'mutex' has been explicitly marked deleted here 30 | mutex(const mutex&) = delete; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:16:58: note: replace 'default' with 'delete' 16 | ForgettingMassCalculator(ForgettingMassCalculator&&) = default; | ^~~~~~~ | delete /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:17:29: warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted] 17 | ForgettingMassCalculator& operator=(ForgettingMassCalculator&&) = default; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:141:14: note: move assignment operator of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move assignment operator 141 | std::mutex ffMutex_; | ^ /usr/include/c++/v1/__mutex/mutex.h:31:10: note: 'operator=' has been explicitly marked deleted here 31 | mutex& operator=(const mutex&) = delete; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:17:69: note: replace 'default' with 'delete' 17 | ForgettingMassCalculator& operator=(ForgettingMassCalculator&&) = default; | ^~~~~~~ | delete In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:120: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:55: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/SAMWriter.hpp:4: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BinWriter.hpp:31:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 31 | BinWriter(std::vector&& bin_data) :_bin_data(move(bin_data)) {}; | ^ | std:: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:120: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:298:62: warning: lambda capture 'invalidScore' is not used [-Wunused-lambda-capture] 298 | [&scores, hardFilter, &msi, decoyThreshold, invalidScore]( | ~~^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:429:10: warning: variable 'locRead' set but not used [-Wunused-but-set-variable] 429 | size_t locRead{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:768:10: warning: variable 'locRead' set but not used [-Wunused-but-set-variable] 768 | size_t locRead{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:826:10: warning: variable 'numMappingsDropped' set but not used [-Wunused-but-set-variable] 826 | size_t numMappingsDropped{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:1237:10: warning: variable 'locRead' set but not used [-Wunused-but-set-variable] 1237 | size_t locRead{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:1240:12: warning: variable 'localNumAssignedFragments' set but not used [-Wunused-but-set-variable] 1240 | uint64_t localNumAssignedFragments{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:1307:10: warning: variable 'numMappingsDropped' set but not used [-Wunused-but-set-variable] 1307 | size_t numMappingsDropped{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:120: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:926:25: warning: lambda capture 'early_stop' is not used [-Wunused-lambda-capture] 926 | &largest_occ, &early_stop, signed_rl, k, signed_k, qidx, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:563:62: note: in instantiation of function template specialization 'salmon::mapping_utils::pasc::map_read' requested here 563 | bool early_exit = salmon::mapping_utils::pasc::map_read(readSubSeq, map_cache_second, PairingStatus::UNPAIRED_RIGHT); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:1730:10: note: in instantiation of function template specialization 'process_reads_sc_sketch' requested here 1730 | process_reads_sc_sketch( | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:2094:5: note: in instantiation of function template specialization 'sc_align_read_library' requested here 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:2521:23: note: in instantiation of function template specialization 'do_sc_align' requested here 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:120: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:926:48: warning: lambda capture 'k' is not used [-Wunused-lambda-capture] 926 | &largest_occ, &early_stop, signed_rl, k, signed_k, qidx, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:927:10: warning: lambda capture 'verbose' is not used [-Wunused-lambda-capture] 927 | verbose](auto& raw_hits, auto& prev_read_pos, auto& max_allowed_occ, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:926:25: warning: lambda capture 'early_stop' is not used [-Wunused-lambda-capture] 926 | &largest_occ, &early_stop, signed_rl, k, signed_k, qidx, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:563:62: note: in instantiation of function template specialization 'salmon::mapping_utils::pasc::map_read' requested here 563 | bool early_exit = salmon::mapping_utils::pasc::map_read(readSubSeq, map_cache_second, PairingStatus::UNPAIRED_RIGHT); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:1730:10: note: in instantiation of function template specialization 'process_reads_sc_sketch' requested here 1730 | process_reads_sc_sketch( | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:2094:5: note: in instantiation of function template specialization 'sc_align_read_library' requested here 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:2521:23: note: in instantiation of function template specialization 'do_sc_align' requested here 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:120: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:926:48: warning: lambda capture 'k' is not used [-Wunused-lambda-capture] 926 | &largest_occ, &early_stop, signed_rl, k, signed_k, qidx, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:927:10: warning: lambda capture 'verbose' is not used [-Wunused-lambda-capture] 927 | verbose](auto& raw_hits, auto& prev_read_pos, auto& max_allowed_occ, | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, std::string &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:2647:27: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 2647 | trueBarcodesIndexMap[ trueBarcodesVec[i] ] = i; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:40: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_map.h:34: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h:377:42: warning: inline function 'tsl::detail_array_hash::array_bucket, unsigned short, true>::append' is not defined [-Wundefined-inline] 377 | const_iterator __attribute__((used)) append(const_iterator end_of_bucket, const CharT* key, size_type key_size, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h:1318:74: note: used here 1318 | std::pair emplace_impl(std::size_t ibucket, typename array_bucket::const_iterator end_of_bucket, | ^ 46 warnings generated. [ 89%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/WhiteList.cpp.o -MF CMakeFiles/salmon.dir/WhiteList.cpp.o.d -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/WhiteList.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/WhiteList.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/WhiteList.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ 2 warnings generated. [ 90%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantify.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:92: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:93: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:17: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:93: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:55: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/SAMWriter.hpp:4: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BinWriter.hpp:31:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 31 | BinWriter(std::vector&& bin_data) :_bin_data(move(bin_data)) {}; | ^ | std:: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:93: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:298:62: warning: lambda capture 'invalidScore' is not used [-Wunused-lambda-capture] 298 | [&scores, hardFilter, &msi, decoyThreshold, invalidScore]( | ~~^~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:103: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:16:3: warning: explicitly defaulted move constructor is implicitly deleted [-Wdefaulted-function-deleted] 16 | ForgettingMassCalculator(ForgettingMassCalculator&&) = default; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:141:14: note: move constructor of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move constructor 141 | std::mutex ffMutex_; | ^ /usr/include/c++/v1/__mutex/mutex.h:30:3: note: 'mutex' has been explicitly marked deleted here 30 | mutex(const mutex&) = delete; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:16:58: note: replace 'default' with 'delete' 16 | ForgettingMassCalculator(ForgettingMassCalculator&&) = default; | ^~~~~~~ | delete /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:17:29: warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted] 17 | ForgettingMassCalculator& operator=(ForgettingMassCalculator&&) = default; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:141:14: note: move assignment operator of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move assignment operator 141 | std::mutex ffMutex_; | ^ /usr/include/c++/v1/__mutex/mutex.h:31:10: note: 'operator=' has been explicitly marked deleted here 31 | mutex& operator=(const mutex&) = delete; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:17:69: note: replace 'default' with 'delete' 17 | ForgettingMassCalculator& operator=(ForgettingMassCalculator&&) = default; | ^~~~~~~ | delete /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:549:14: warning: variable 'auxProbSum' set but not used [-Wunused-but-set-variable] 549 | double auxProbSum{0.0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:824:10: warning: variable 'locRead' set but not used [-Wunused-but-set-variable] 824 | size_t locRead{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:827:12: warning: variable 'localNumAssignedFragments' set but not used [-Wunused-but-set-variable] 827 | uint64_t localNumAssignedFragments{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:1657:10: warning: variable 'locRead' set but not used [-Wunused-but-set-variable] 1657 | size_t locRead{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:93: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:93: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:93: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:93: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ 34 warnings generated. [ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ 12 warnings generated. [ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentStartPositionDistribution.cpp [ 92%] Building CXX object src/CMakeFiles/salmon.dir/GZipWriter.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/GZipWriter.cpp.o -MF CMakeFiles/salmon.dir/GZipWriter.cpp.o.d -o CMakeFiles/salmon.dir/GZipWriter.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.hpp:145: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.tpp:609:12: warning: variable 'n' set but not used [-Wunused-but-set-variable] 609 | size_t n{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:17: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 252 | : std::integral_constant>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant>' requested here 254 | is_trivially_destructible::value> {}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1818:32: note: in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:259:17: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1819:22: note: in instantiation of template class 'phmap::is_trivially_copy_assignable>' requested here 1819 | phmap::is_trivially_copy_assignable>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GZipWriter.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ 30 warnings generated. [ 93%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantMerge.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantMerge.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantMerge.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantMerge.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantMerge.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ 13 warnings generated. [ 94%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -MF CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o.d -o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ProgramOptionsGenerator.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ProgramOptionsGenerator.cpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ProgramOptionsGenerator.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ProgramOptionsGenerator.cpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ProgramOptionsGenerator.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ 11 warnings generated. [ 95%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/FASTAParser.cpp.o -MF CMakeFiles/salmon.dir/FASTAParser.cpp.o.d -o CMakeFiles/salmon.dir/FASTAParser.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hpp:35: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:8: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] 647 | mer_base_static(unsigned int k, const char* s) : super(k_) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hpp:35: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:117:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 117 | __int128_ns::__print(os, x); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 102 | char padding[nb_padding]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:123:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 123 | __int128_ns::__print(os, x); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 102 | char padding[nb_padding]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ 23 warnings generated. [ 96%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o -MF CMakeFiles/salmon.dir/AlignmentModel.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentModel.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:20:31: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 20 | transitionProbsLeft_[i] = std::move(AtomicMatrix( | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:20:31: note: remove std::move call here 20 | transitionProbsLeft_[i] = std::move(AtomicMatrix( | ^~~~~~~~~~ 21 | numAlignmentStates(), numAlignmentStates(), alpha)); | ~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:22:32: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 22 | transitionProbsRight_[i] = std::move(AtomicMatrix( | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:22:32: note: remove std::move call here 22 | transitionProbsRight_[i] = std::move(AtomicMatrix( | ^~~~~~~~~~ 23 | numAlignmentStates(), numAlignmentStates(), alpha)); | ~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:96:33: warning: unused parameter 'primary' [-Wunused-parameter] 96 | bam_seq_t* read, bam_seq_t* primary, Transcript& ref, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:230:75: warning: unused parameter 'primary' [-Wunused-parameter] 230 | double AlignmentModel::logLikelihood(const ReadPair& hit, const ReadPair& primary, Transcript& ref) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:429:66: warning: unused parameter 'primary' [-Wunused-parameter] 429 | void AlignmentModel::update(const ReadPair& hit, const ReadPair& primary, | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ 24 warnings generated. [ 96%] Building CXX object src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -MF CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o.d -o CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:17:45: warning: unused parameter 'alpha' [-Wunused-parameter] 17 | ONTAlignmentModel::ONTAlignmentModel(double alpha, uint32_t readBins) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:53:22: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare] 53 | if(counts.sclips() >= cigarRLen) | ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:137:56: warning: unused parameter 'p' [-Wunused-parameter] 137 | Transcript& ref, double p, double mass) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:194:50: warning: unused parameter 'os' [-Wunused-parameter] 194 | void ONTAlignmentModel::printModel(std::ostream& os) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ 23 warnings generated. [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -MF CMakeFiles/salmon.dir/AlignmentCommon.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ 19 warnings generated. [ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.hpp:145: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.tpp:609:12: warning: variable 'n' set but not used [-Wunused-but-set-variable] 609 | size_t n{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:17: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 252 | : std::integral_constant>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant>' requested here 254 | is_trivially_destructible::value> {}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1818:32: note: in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:259:17: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1819:22: note: in instantiation of template class 'phmap::is_trivially_copy_assignable>' requested here 1819 | phmap::is_trivially_copy_assignable>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:39: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/MiniBatchInfo.hpp:28:12: warning: variable 'ng' set but not used [-Wunused-but-set-variable] 28 | size_t ng{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:49: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedEMOptimizer.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:52: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:16:3: warning: explicitly defaulted move constructor is implicitly deleted [-Wdefaulted-function-deleted] 16 | ForgettingMassCalculator(ForgettingMassCalculator&&) = default; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:141:14: note: move constructor of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move constructor 141 | std::mutex ffMutex_; | ^ /usr/include/c++/v1/__mutex/mutex.h:30:3: note: 'mutex' has been explicitly marked deleted here 30 | mutex(const mutex&) = delete; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:16:58: note: replace 'default' with 'delete' 16 | ForgettingMassCalculator(ForgettingMassCalculator&&) = default; | ^~~~~~~ | delete /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:17:29: warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted] 17 | ForgettingMassCalculator& operator=(ForgettingMassCalculator&&) = default; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:141:14: note: move assignment operator of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move assignment operator 141 | std::mutex ffMutex_; | ^ /usr/include/c++/v1/__mutex/mutex.h:31:10: note: 'operator=' has been explicitly marked deleted here 31 | mutex& operator=(const mutex&) = delete; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:17:69: note: replace 'default' with 'delete' 17 | ForgettingMassCalculator& operator=(ForgettingMassCalculator&&) = default; | ^~~~~~~ | delete /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:403:11: warning: variable 'sidx' set but not used [-Wunused-but-set-variable] 403 | int sidx{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:577:14: warning: variable 'auxProbSum' set but not used [-Wunused-but-set-variable] 577 | double auxProbSum{0.0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ 35 warnings generated. [ 99%] Building CXX object src/CMakeFiles/salmon.dir/BAMUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/BAMUtils.cpp.o -MF CMakeFiles/salmon.dir/BAMUtils.cpp.o.d -o CMakeFiles/salmon.dir/BAMUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BAMUtils.cpp [100%] Linking CXX executable salmon cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/salmon.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto=thin -lpthread -fstack-protector-strong -Xlinker --dependency-file=CMakeFiles/salmon.dir/link.d CMakeFiles/salmon.dir/EMUtils.cpp.o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o CMakeFiles/salmon.dir/Salmon.cpp.o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o CMakeFiles/salmon.dir/Graph.cpp.o CMakeFiles/salmon.dir/DedupUMI.cpp.o CMakeFiles/salmon.dir/Alevin.cpp.o CMakeFiles/salmon.dir/AlevinHash.cpp.o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o CMakeFiles/salmon.dir/WhiteList.cpp.o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o CMakeFiles/salmon.dir/GZipWriter.cpp.o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o CMakeFiles/salmon.dir/FASTAParser.cpp.o CMakeFiles/salmon.dir/AlignmentModel.cpp.o CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o CMakeFiles/salmon.dir/BAMUtils.cpp.o -o salmon -L/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/lib -L/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib -L/usr/local/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib:/usr/local/lib" ../external/pufferfish/src/libpuffer.a libsalmon_core.a ../external/pufferfish/external/twopaco/graphconstructor/libtwopaco.a ../external/pufferfish/external/twopaco/graphdump/libgraphdump.a ../external/pufferfish/external/ntcard/libntcard.a -lgff /usr/local/lib/libboost_iostreams.a /usr/local/lib/libboost_system.a /usr/local/lib/libboost_filesystem.a /usr/local/lib/libboost_timer.a /usr/local/lib/libboost_chrono.a /usr/local/lib/libboost_program_options.a /usr/local/lib/libboost_regex.a /usr/local/lib/libcurl.a /usr/lib/libz.a -lm /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a /usr/lib/liblzma.a /usr/lib/libmd.a /usr/lib/libbz2.a -lgomp ../external/pufferfish/src/libksw2pp.a libalevin_core.a -lc /usr/local/lib/libtbb.so.12.15 /usr/local/lib/libtbbmalloc.so.2.15 -lrt gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [100%] Built target salmon gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles 0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for salmon-1.10.2_7 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/salmon/work/.build/src/salmon /wrkdirs/usr/ports/biology/salmon/work/stage/usr/local/bin ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-05-03T15:54:18+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=fa53920e72' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for salmon-1.10.2_7 ===> Building salmon-1.10.2_7 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for salmon-1.10.2_7 build of biology/salmon | salmon-1.10.2_7 ended at Sat May 3 17:13:07 BST 2025 build time: 00:18:50