=>> Building biology/salmon build started at Fri Apr 5 16:03:59 BST 2024 port directory: /usr/ports/biology/salmon package name: salmon-1.10.2_2 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1506 Dec 2 20:29 /usr/ports/biology/salmon/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: cf5d9b8b96 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 09 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-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/13-amd64-default-dan/09/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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=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=/ccache/libexec/ccache:/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" CCACHE_DIR="/root/.ccache" --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=/ccache/libexec/ccache:/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 DONTSTRIP=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-pipe -g -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="-pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -m 555" BSD_INSTALL_LIB="install -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="debug" OSREL=13.2 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 mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/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 --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_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> salmon-1.10.2_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of salmon-1.10.2_2 =========================================================================== =================================================== ===== 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_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by salmon-1.10.2_2 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_2 for building ===> Extracting for salmon-1.10.2_2 => 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_2 ===> Applying FreeBSD patches for salmon-1.10.2_2 from /usr/ports/biology/salmon/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.2_2 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.26_1.pkg [pkg-builder.dan.net.uk] Installing bash-5.2.26_1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting bash-5.2.26_1: .......... done ===> salmon-1.10.2_2 depends on executable: bash - found ===> Returning to build of salmon-1.10.2_2 ===> salmon-1.10.2_2 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-1.84.0... [pkg-builder.dan.net.uk] | `-- Installing icu-74.2,1... [pkg-builder.dan.net.uk] | `-- Extracting icu-74.2,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting boost-libs-1.84.0: .......... done [pkg-builder.dan.net.uk] Extracting cereal-1.3.2_1: .......... done ===== Message from boost-libs-1.84.0: -- 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_2 depends on package: cereal>=1.3.0 - found ===> Returning to build of salmon-1.10.2_2 ===> salmon-1.10.2_2 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_2 depends on package: libgff==2.0.0 - found ===> Returning to build of salmon-1.10.2_2 ===> salmon-1.10.2_2 depends on executable: libtool - not found ===> Installing existing package /packages/All/libtool-2.4.7_2.pkg [pkg-builder.dan.net.uk] Installing libtool-2.4.7_2... [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-2.4.7_2: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> salmon-1.10.2_2 depends on executable: libtool - found ===> Returning to build of salmon-1.10.2_2 ===> salmon-1.10.2_2 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_1... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_1: .......... done [pkg-builder.dan.net.uk] Extracting autoconf-2.72: .......... done ===> salmon-1.10.2_2 depends on executable: autoreconf - found ===> Returning to build of salmon-1.10.2_2 ===> salmon-1.10.2_2 depends on executable: aclocal - not found ===> Installing existing package /packages/All/automake-1.16.5_1.pkg [pkg-builder.dan.net.uk] Installing automake-1.16.5_1... [pkg-builder.dan.net.uk] Extracting automake-1.16.5_1: .......... done ===> salmon-1.10.2_2 depends on executable: aclocal - found ===> Returning to build of salmon-1.10.2_2 ===> salmon-1.10.2_2 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.28.3... [pkg-builder.dan.net.uk] `-- Installing expat-2.6.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.5... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.5: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.48.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.48.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... 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-3.28.3: .......... done ===> salmon-1.10.2_2 depends on file: /usr/local/bin/cmake - found ===> Returning to build of salmon-1.10.2_2 ===> salmon-1.10.2_2 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_2 depends on package: gmake>=4.4.1 - found ===> Returning to build of salmon-1.10.2_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.2_2 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> salmon-1.10.2_2 depends on shared library: libtbb.so - not found ===> Installing existing package /packages/All/onetbb-2021.11.0.pkg [pkg-builder.dan.net.uk] Installing onetbb-2021.11.0... [pkg-builder.dan.net.uk] `-- Installing hwloc2-2.8.0_1... [pkg-builder.dan.net.uk] | `-- Installing level-zero-1.16.1... [pkg-builder.dan.net.uk] | `-- Extracting level-zero-1.16.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libpciaccess-0.18... [pkg-builder.dan.net.uk] | `-- Extracting libpciaccess-0.18: ..... done [pkg-builder.dan.net.uk] | `-- Installing libxml2-2.11.7... [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libxml2-2.11.7: .......... done [pkg-builder.dan.net.uk] `-- Extracting hwloc2-2.8.0_1: .......... done [pkg-builder.dan.net.uk] Extracting onetbb-2021.11.0: .......... done ===> salmon-1.10.2_2 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so) ===> Returning to build of salmon-1.10.2_2 ===> salmon-1.10.2_2 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-8.6.0.pkg [pkg-builder.dan.net.uk] Installing curl-8.6.0... [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 libidn2-2.3.7... [pkg-builder.dan.net.uk] | `-- Installing libunistring-1.2... [pkg-builder.dan.net.uk] | `-- Extracting libunistring-1.2: .......... done [pkg-builder.dan.net.uk] `-- Extracting libidn2-2.3.7: .......... done [pkg-builder.dan.net.uk] `-- Installing libnghttp2-1.60.0... [pkg-builder.dan.net.uk] `-- Extracting libnghttp2-1.60.0: ....... done [pkg-builder.dan.net.uk] `-- Installing librtmp-2.4.20190330_1... [pkg-builder.dan.net.uk] `-- Extracting librtmp-2.4.20190330_1: ......... done [pkg-builder.dan.net.uk] `-- Installing libssh2-1.11.0_1,3... [pkg-builder.dan.net.uk] `-- Extracting libssh2-1.11.0_1,3: .......... done [pkg-builder.dan.net.uk] `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] Extracting curl-8.6.0: .......... done ===> salmon-1.10.2_2 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of salmon-1.10.2_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for salmon-1.10.2_2 (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 14.0.5 -- The CXX compiler identification is Clang 14.0.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /ccache/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: /ccache/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 = Debug -- 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 Debug 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 "1.2.13") -- 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. -- Found Boost: /usr/local/include (found suitable version "1.84.0", 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 "2021.11.0", minimum required is "2021.4") FOUND SUITABLE TBB VERSION : 2021.11.0 -- libgff ver. 2.0.0 found. -- include: /usr/local/include/ -- lib : /usr/local/lib/ -- Found CURL: /usr/local/lib/libcurl.a (found version "8.6.0") 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: /ccache/libexec/ccache/cc CC version: version: 1.0.0 Building basic pufferfish components for salmon setting -DHAVE_NUMERIC_LIMITS128 -- setting COMPACT_VECTOR_DIR for graphdump to be /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump 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.12.11;/usr/local/lib/libtbbbind_2_0.so;/usr/local/lib/libtbbbind_2_0.so.3;/usr/local/lib/libtbbbind_2_0.so.3.11;/usr/local/lib/libtbbmalloc.so;/usr/local/lib/libtbbmalloc.so.2;/usr/local/lib/libtbbmalloc.so.2.11;/usr/local/lib/libtbbmalloc_proxy.so;/usr/local/lib/libtbbmalloc_proxy.so.2;/usr/local/lib/libtbbmalloc_proxy.so.2.11 -- Configuring done (6.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_RELEASE 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_2 /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 gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' 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' 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=/ccache/libexec/ccache/cc CXX=/ccache/libexec/ccache/c++ checking for a BSD-compatible install... install: DONTSTRIP set - will not strip installed binaries /usr/bin/install -c 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 whether to enable maintainer-specific portions of Makefiles... no checking for gcc... /ccache/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 /ccache/libexec/ccache/cc accepts -g... yes checking for /ccache/libexec/ccache/cc option to enable C11 features... none needed checking whether /ccache/libexec/ccache/cc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of /ccache/libexec/ccache/cc... gcc3 checking build system type... amd64-unknown-freebsd13.2 checking host system type... amd64-unknown-freebsd13.2 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 /ccache/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-freebsd13.2 file names to amd64-unknown-freebsd13.2 format... func_convert_file_noop checking how to convert amd64-unknown-freebsd13.2 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... no 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 ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from /ccache/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 /ccache/libexec/ccache/cc supports -fno-rtti -fno-exceptions... yes checking for /ccache/libexec/ccache/cc option to produce PIC... -fPIC -DPIC checking if /ccache/libexec/ccache/cc PIC flag -fPIC -DPIC works... yes checking if /ccache/libexec/ccache/cc static flag -static works... yes checking if /ccache/libexec/ccache/cc supports -c -o file.o... yes checking if /ccache/libexec/ccache/cc supports -c -o file.o... (cached) yes checking whether the /ccache/libexec/ccache/cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd13.2 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 /ccache/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=/ccache/libexec/ccache/cc' 'CXX=/ccache/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... install: DONTSTRIP set - will not strip installed binaries /usr/bin/install -c 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 whether to enable maintainer-specific portions of Makefiles... no checking for gcc... /ccache/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 /ccache/libexec/ccache/cc accepts -g... yes checking for /ccache/libexec/ccache/cc option to enable C11 features... none needed checking whether /ccache/libexec/ccache/cc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of /ccache/libexec/ccache/cc... gcc3 checking build system type... amd64-unknown-freebsd13.2 checking host system type... amd64-unknown-freebsd13.2 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 /ccache/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-freebsd13.2 file names to amd64-unknown-freebsd13.2 format... func_convert_file_noop checking how to convert amd64-unknown-freebsd13.2 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... no 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 ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from /ccache/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 /ccache/libexec/ccache/cc supports -fno-rtti -fno-exceptions... yes checking for /ccache/libexec/ccache/cc option to produce PIC... -fPIC -DPIC checking if /ccache/libexec/ccache/cc PIC flag -fPIC -DPIC works... yes checking if /ccache/libexec/ccache/cc static flag -static works... yes checking if /ccache/libexec/ccache/cc supports -c -o file.o... yes checking if /ccache/libexec/ccache/cc supports -c -o file.o... (cached) yes checking whether the /ccache/libexec/ccache/cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd13.2 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: /ccache/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=/ccache/libexec/ccache/cc CXX=/ccache/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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -pipe -g -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: /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem 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compile: /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -pipe -g -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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -pipe -g -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: /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -pipe -g -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 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.deps/htscodecs.Plo /bin/sh ../libtool --tag=CC --mode=compile /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -pipe -g -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: /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -pipe -g -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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -msse4.1 -mssse3 -mpopcnt -pipe -g -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: /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -msse4.1 -mssse3 -mpopcnt -pipe -g -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 /ccache/libexec/ccache/cc -msse4.1 -mssse3 -mpopcnt -pipe -g -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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx2 -pipe -g -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: /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx2 -pipe 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ln -s "../librANS_static32x16pr_avx2.la" "librANS_static32x16pr_avx2.la" ) /bin/sh ../libtool --tag=CC --mode=compile /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx512f -pipe -g -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: /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx512f -pipe -g -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 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"/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]: 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-L/usr/local/lib libtool: link: /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o srf_list srf_list.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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT hash_exp.o -MD -MP -MF .deps/hash_exp.Tpo -c -o hash_exp.o hash_exp.c mv -f .deps/hash_exp.Tpo .deps/hash_exp.Po /bin/sh ../libtool --tag=CC --mode=link /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o hash_exp hash_exp.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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cram_dump.o -MD -MP -MF .deps/cram_dump.Tpo -c -o cram_dump.o cram_dump.c mv -f .deps/cram_dump.Tpo .deps/cram_dump.Po /bin/sh ../libtool --tag=CC --mode=link /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_dump cram_dump.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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cram_index.o -MD -MP -MF .deps/cram_index.Tpo -c -o cram_index.o cram_index.c mv -f .deps/cram_index.Tpo .deps/cram_index.Po /bin/sh ../libtool --tag=CC --mode=link /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_index cram_index.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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scramble.o -MD -MP -MF .deps/scramble.Tpo -c -o scramble.o scramble.c mv -f .deps/scramble.Tpo .deps/scramble.Po /bin/sh ../libtool --tag=CC --mode=link /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scramble scramble.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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scram_merge.o -MD -MP -MF .deps/scram_merge.Tpo -c -o scram_merge.o scram_merge.c mv -f .deps/scram_merge.Tpo .deps/scram_merge.Po /bin/sh ../libtool --tag=CC --mode=link /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scram_merge scram_merge.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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scram_pileup.o -MD -MP -MF .deps/scram_pileup.Tpo -c -o scram_pileup.o scram_pileup.c mv -f .deps/scram_pileup.Tpo .deps/scram_pileup.Po /bin/sh ../libtool --tag=CC --mode=link /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scram_pileup scram_pileup.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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scram_flagstat.o -MD -MP -MF .deps/scram_flagstat.Tpo -c -o scram_flagstat.o scram_flagstat.c mv -f .deps/scram_flagstat.Tpo .deps/scram_flagstat.Po /bin/sh ../libtool --tag=CC --mode=link /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scram_flagstat scram_flagstat.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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scram_test.o -MD -MP -MF .deps/scram_test.Tpo -c -o scram_test.o scram_test.c mv -f .deps/scram_test.Tpo .deps/scram_test.Po /bin/sh ../libtool --tag=CC --mode=link /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /ccache/libexec/ccache/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scram_test scram_test.o 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-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 /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -pipe -g -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 /ccache/libexec/ccache/cc -pipe -g -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: /ccache/libexec/ccache/cc -pipe -g -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' /ccache/libexec/ccache/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -pipe -g -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 /ccache/libexec/ccache/cc -pipe -g -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: /ccache/libexec/ccache/cc -pipe -g -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 install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c .libs/libhtscodecs.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a install: DONTSTRIP set - will not strip installed binaries 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' install: DONTSTRIP set - will not strip installed binaries 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 install: DONTSTRIP set - will not strip installed binaries 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 install: DONTSTRIP set - will not strip installed binaries 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 install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c makeSCF /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/makeSCF install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c extract_seq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_seq install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c extract_qual /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_qual install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c extract_fastq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_fastq install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c index_tar /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/index_tar install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c scf_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_dump install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c scf_info /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_info install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c scf_update /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_update install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c get_comment /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/get_comment install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c hash_tar /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_tar install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c hash_extract /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_extract install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c hash_list /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_list install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c trace_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/trace_dump install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c hash_sff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_sff install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c append_sff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/append_sff install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c ztr_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/ztr_dump install: DONTSTRIP set - will not strip installed binaries 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 install: DONTSTRIP set - will not strip installed binaries 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 install: DONTSTRIP set - will not strip installed binaries 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 install: DONTSTRIP set - will not strip installed binaries 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 install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c srf2fastq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf2fastq install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c srf2fasta /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf2fasta install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c srf_filter /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_filter install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c srf_info /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_info install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c srf_list /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_list install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c hash_exp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_exp install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c cram_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_dump install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c cram_index /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_index install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c scramble /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scramble install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c scram_merge /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_merge install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c scram_pileup /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_pileup install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c scram_flagstat /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_flagstat install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c scram_test /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_test install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c cram_size /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_size install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c cram_filter /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_filter install: DONTSTRIP set - will not strip installed binaries 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' install: DONTSTRIP set - will not strip installed binaries 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' install: DONTSTRIP set - will not strip installed binaries 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' install: DONTSTRIP set - will not strip installed binaries 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' install: DONTSTRIP set - will not strip installed binaries 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 io_lib/cram_index.h io_lib/cram_stats.h io_lib/cram_bambam.h '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/io_lib' install: DONTSTRIP set - will not strip installed binaries /usr/bin/install -c -m 644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h io_lib/version.h '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/io_lib' install: DONTSTRIP set - will not strip installed binaries 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-install [ 7%] Completed '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 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' 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 && /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -MF CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o.d -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common/SignalHandler.cpp [ 8%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard && /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -MF CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o.d -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common/Fcontrol.cpp [ 9%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard && /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o -MF CMakeFiles/ntcard.dir/nthll.cpp.o.d -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/nthll.cpp [ 10%] Linking CXX static library libntcard.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard && /usr/local/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o /usr/bin/llvm-ranlib libntcard.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 10%] Built target ntcard gmake -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.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/graphdump /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphdump 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-fno-strict-aliasing -isystem /usr/local/include -pipe -g -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 && /ccache/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/. -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -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 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 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-I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -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/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 && /ccache/libexec/ccache/c++ 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/usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -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.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/common.cpp [ 22%] Linking CXX static library libtwopaco.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/local/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libtwopaco.a CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o /usr/bin/llvm-ranlib libtwopaco.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 22%] Built target twopaco gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.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_sse2.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 23%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /ccache/libexec/ccache/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O3 -msse -msse2 -mno-sse4.1 -MD 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gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 25%] Built target ksw2pp_sse2 gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.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_sse4.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build gmake[2]: 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/ccache/libexec/ccache/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 27%] Built target ksw2pp_sse4 gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.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_basic.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 27%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /ccache/libexec/ccache/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/kalloc.c [ 28%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /ccache/libexec/ccache/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extd.c [ 29%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /ccache/libexec/ccache/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c 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/wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /ccache/libexec/ccache/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -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 && /ccache/libexec/ccache/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -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 && /ccache/libexec/ccache/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 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' 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" cr 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 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' 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] #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] 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] 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 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] size_t totalKmersIshouldSee{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] 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 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 _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 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 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 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 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] 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 ? 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 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] 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 ? 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 (*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] 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 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 _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 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 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 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 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] 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 ? 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 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] 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 ? 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 posVec[idx] = kb1.pos(); ^ 17 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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] 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] 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] 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] 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] 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] 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] 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] #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: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] 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 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 template class PufferfishBaseIndex; ^ 9 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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] #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: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] 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] 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] 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] 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] 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] 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] 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] 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] 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 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 auto contigIterRange = contigRange(rank); ^ 10 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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] #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: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] 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] 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] 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] 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] 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] 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] 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] 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 auto sampledPos = sampledPos_[currRank]; ^ 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] 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 ? 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 if (presenceVec_[idx] == 1) { ^ 10 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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] #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: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] 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] 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] 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] 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] 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] 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] 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] 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 ? 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 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] 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 ? 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 pos = sampledPos_[currRank]; ^ 10 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] [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] 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] 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] auto orphanFiller = [&jointMemsList, &maxCoverage, &coverageRatio, &maxLeftOrRight, &leftOrphan, &rightOrphan, thresh, ithresh, orphan_chain_sub_thresh] ~~^~~~~~~ 11 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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] 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] 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] 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] 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] 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] 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] void bits(unsigned b) { } // NOOP ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9sel.cpp:207:41: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf( "i: %lld s: %lld r: %lld\n", i, t, r ); ~~~~ ^ %lu /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9sel.cpp:207:44: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf( "i: %lld s: %lld r: %lld\n", i, t, r ); ~~~~ ^ %lu /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9sel.cpp:207:47: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf( "i: %lld s: %lld r: %lld\n", i, t, r ); ~~~~ ^ %lu /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9sel.cpp:217:42: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf( "i: %lld r: %lld s: %lld\n", i, r, t ); ~~~~ ^ %lu /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9sel.cpp:217:45: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf( "i: %lld r: %lld s: %lld\n", i, r, t ); ~~~~ ^ %lu /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9sel.cpp:217:48: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf( "i: %lld r: %lld s: %lld\n", i, r, t ); ~~~~ ^ %lu 13 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] 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] #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] 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 ? 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 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 return doPufferfishInternalValidate(pi, validateOpts); ^ 10 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] 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] #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] 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 ? 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 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] 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 ? 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 << " contigOffsets size: " << contigOffsets_.size() << ", bpe: " << bits_per_element << " , total elements in the contig table: " << contigOffsets_[contigOffsets_.size()-1] << "\n"; ^ 11 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] 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] #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] std::vector get_kmers(const std::string& fasta_file, uint32_t k) { ^ 10 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ 8 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ 8 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 ? 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 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] 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 ? 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 (*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] 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 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 _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 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 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 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 eqID = eqMap[tlist]; ^ 12 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -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 -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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] 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: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] 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] 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 auto it = dset.insert(dname); ^ 5 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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] #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: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] 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] 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] 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] 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] 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] 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] void bits(unsigned b) { } // NOOP ^ 8 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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] #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: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] 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] 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] 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] 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] 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] 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] void bits(unsigned b) { } // NOOP ^ 8 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] uint32_t k; ^ 8 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ 8 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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: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] 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] 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] 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] 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] 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] 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] 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] #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] 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 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 _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 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 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 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 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] 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 ? 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 uint8_t edgeVec = edges[contig.contigIdx_] ; ^ 10 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -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 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' 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 [ 56%] Building CXX object src/CMakeFiles/salmon_core.dir/backtrace.cc.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -flto=thin -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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: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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 _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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 _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] 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, false>>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::div_assign_op>' requested here 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, false>>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::div_assign_op, 0>' requested here 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, false>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 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, false>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op, Eigen::internal::Dense2Dense>::run' requested here 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, false>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 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, false>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 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, false>>::operator/=' requested here _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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 _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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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 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 _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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 void SBModel::combineCounts(const SBModel& other) { _probs += other._probs; } ^ 6 warnings generated. [ 63%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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: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] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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>, 2>>, Eigen::internal::swap_assign_op>' requested here 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>, 2>>, Eigen::internal::swap_assign_op, 1>' requested here : 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>, 2>>, Eigen::internal::swap_assign_op, 0>' requested here 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>, 2>, Eigen::internal::swap_assign_op>' requested here 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>, 2>, Eigen::internal::swap_assign_op, Eigen::internal::Dense2Dense>::run' requested here 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>, 2>, Eigen::internal::swap_assign_op>' requested here 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>, 2>, Eigen::internal::swap_assign_op>' requested here 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>, 2>>' requested here 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 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] 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, false>>, Eigen::internal::evaluator, -1, 1, true>, -1, 1, false>, 2>>, Eigen::internal::swap_assign_op>' requested here 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, false>>, Eigen::internal::evaluator, -1, 1, true>, -1, 1, false>, 2>>, Eigen::internal::swap_assign_op, 1>' requested here : 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, false>>, Eigen::internal::evaluator, -1, 1, true>, -1, 1, false>, 2>>, Eigen::internal::swap_assign_op, 0>' requested here 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, false>, Eigen::Reverse, -1, 1, true>, -1, 1, false>, 2>, Eigen::internal::swap_assign_op>' requested here 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, false>, Eigen::Reverse, -1, 1, true>, -1, 1, false>, 2>, Eigen::internal::swap_assign_op, Eigen::internal::Dense2Dense>::run' requested here 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, false>, Eigen::Reverse, -1, 1, true>, -1, 1, false>, 2>, Eigen::internal::swap_assign_op>' requested here 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, false>, Eigen::Reverse, -1, 1, true>, -1, 1, false>, 2>, Eigen::internal::swap_assign_op>' requested here 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, false>>::swap, -1, 1, true>, -1, 1, false>, 2>>' requested here 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 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] 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, false>>, Eigen::internal::evaluator, -1, 1, false>, 2>>, Eigen::internal::swap_assign_op>' requested here 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, false>>, Eigen::internal::evaluator, -1, 1, false>, 2>>, Eigen::internal::swap_assign_op, 1>' requested here : 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, false>>, Eigen::internal::evaluator, -1, 1, false>, 2>>, Eigen::internal::swap_assign_op, 0>' requested here 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, false>, Eigen::Reverse, -1, 1, false>, 2>, Eigen::internal::swap_assign_op>' requested here 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, false>, Eigen::Reverse, -1, 1, false>, 2>, Eigen::internal::swap_assign_op, Eigen::internal::Dense2Dense>::run' requested here 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, false>, Eigen::Reverse, -1, 1, false>, 2>, Eigen::internal::swap_assign_op>' requested here 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, false>, Eigen::Reverse, -1, 1, false>, 2>, Eigen::internal::swap_assign_op>' requested here 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, false>>::swap, -1, 1, false>, 2>>' requested here 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 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] 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, false>, -1, 1, false>>, Eigen::internal::evaluator, 1, 1, false>, -1, 1, false>, 2>>, Eigen::internal::swap_assign_op>' requested here 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, false>, -1, 1, false>>, Eigen::internal::evaluator, 1, 1, false>, -1, 1, false>, 2>>, Eigen::internal::swap_assign_op, 1>' requested here : 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, false>, -1, 1, false>>, Eigen::internal::evaluator, 1, 1, false>, -1, 1, false>, 2>>, Eigen::internal::swap_assign_op, 0>' requested here 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, false>, -1, 1, false>, Eigen::Reverse, 1, 1, false>, -1, 1, false>, 2>, Eigen::internal::swap_assign_op>' requested here 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, false>, -1, 1, false>, Eigen::Reverse, 1, 1, false>, -1, 1, false>, 2>, Eigen::internal::swap_assign_op, Eigen::internal::Dense2Dense>::run' requested here 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, false>, -1, 1, false>, Eigen::Reverse, 1, 1, false>, -1, 1, false>, 2>, Eigen::internal::swap_assign_op>' requested here 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, false>, -1, 1, false>, Eigen::Reverse, 1, 1, false>, -1, 1, false>, 2>, Eigen::internal::swap_assign_op>' requested here 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, false>, -1, 1, false>>::swap, 1, 1, false>, -1, 1, false>, 2>>' requested here 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 return effLensOut; ^ 10 warnings generated. [ 65%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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: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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 GCFragModel(GCFragModel&&) = default; ^ 3 warnings generated. [ 66%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 && /ccache/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 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CMakeFiles/salmon_core.dir/SGSmooth.cpp.o.d -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SGSmooth.cpp [ 69%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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" cr 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 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" /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/alevin_core.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 71%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=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 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CMakeFiles/alevin_core.dir/edlib.cpp.o.d -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/edlib.cpp [ 72%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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/SingleCellProtocols.cpp.o -MF CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o.d -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SingleCellProtocols.cpp [ 73%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -flto=thin -g -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 [ 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" cr 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 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 /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/UnitTestsMain.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 73%] Building CXX object src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -g -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/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -MF CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o.d -o CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/UnitTests.cpp [ 74%] Linking CXX static library libUnitTestsMain.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -P CMakeFiles/UnitTestsMain.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/UnitTestsMain.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libUnitTestsMain.a CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o /usr/bin/llvm-ranlib libUnitTestsMain.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 74%] Built target UnitTestsMain gmake -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.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/unitTests.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 75%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -g -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/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 [ 76%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -g -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 && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -g -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: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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 GCFragModel(GCFragModel&&) = default; ^ 3 warnings generated. [ 78%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -g -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: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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 GCFragModel(GCFragModel&&) = default; ^ 3 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 /ccache/libexec/ccache/c++ -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -lpthread -fstack-protector-strong 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.12.11 /usr/local/lib/libtbbmalloc.so.2.11 -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 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' 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 && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: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] 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] 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] 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] 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] 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] 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] 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] 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 gcBitArray_[i] = 1; ^ 15 warnings generated. [ 81%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] 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] 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: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] 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] 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] 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] 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] 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] 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] 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] 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: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] #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] 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] 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] 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] [&eqVec, &alphaIn, &alphaOut, ^ /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 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] [&eqVec, &priorAlphas, &alphaIn, &alphaOut](const BlockedIndexRange& range) -> void { ^ /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 EMUpdate_(arena, eqVec, priorAlphas, alphas, alphasPrime); ^ 25 warnings generated. [ 82%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] #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] 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] 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 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] 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 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 _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 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 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 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 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] 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 std::pair emplace_impl(std::size_t ibucket, typename array_bucket::const_iterator end_of_bucket, ^ 28 warnings generated. [ 82%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] 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] 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: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] 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] 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] 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] 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] 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] 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] 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] 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: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] #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] 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] 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] [&, beta](const BlockedIndexRange& range) -> void { ^ /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 sampleRoundNonCollapsedMultithreaded_( ^ 23 warnings generated. [ 83%] Building CXX object src/CMakeFiles/salmon.dir/Salmon.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] #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: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] 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] 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] 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] 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] 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] 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] 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] void serialize(Archive& ar, const unsigned int version) { ^ 9 warnings generated. [ 84%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] #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: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] 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] 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] 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] 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] 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] 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] 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] 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 gcBitArray_[i] = 1; ^ 16 warnings generated. [ 85%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] 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] 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: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] 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] 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] 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] 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] 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] 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] 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] 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 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] 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 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 _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 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 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 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 index = vertMap[node]; ^ 13 warnings generated. [ 86%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] 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] 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: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] 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] 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] 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] 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] 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] 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] 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] 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] #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] 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 vertexIndices[gene] = gid; ^ 29 warnings generated. [ 87%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] 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] 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: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] 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] 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] 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] 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] 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] 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] 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] 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] #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, allocator>') [-Wrange-loop-construct] 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, allocator> &') to prevent copying 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 std::__hash_const_iterator *>::value_type' (aka 'const std::string') [-Wrange-loop-construct] 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 std::__hash_const_iterator *>::value_type &' (aka 'const std::string &') to prevent copying 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 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] 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 std::pair emplace_impl(std::size_t ibucket, typename array_bucket::const_iterator end_of_bucket, ^ 25 warnings generated. [ 87%] Building CXX object src/CMakeFiles/salmon.dir/AlevinHash.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] 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] 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: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] 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] 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] 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] 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] 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] 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] 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] 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] #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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 std::pair emplace_impl(std::size_t ibucket, typename array_bucket::const_iterator end_of_bucket, ^ 27 warnings generated. [ 88%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] 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] 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: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] 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] 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] 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] 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] 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] 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] 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] 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] #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] 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 std::mutex ffMutex_; ^ /usr/include/c++/v1/__mutex_base:40:5: note: 'mutex' has been explicitly marked deleted here mutex(const mutex&) = delete; ^ 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:17:29: warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted] 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 std::mutex ffMutex_; ^ /usr/include/c++/v1/__mutex_base:41:12: note: 'operator=' has been explicitly marked deleted here mutex& operator=(const mutex&) = delete; ^ 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] [&scores, hardFilter, &msi, decoyThreshold, invalidScore]( ~~^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] IndexT* qidx, std::vector& transcripts, ^ /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] size_t numMappingsDropped{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] size_t numMappingsDropped{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] uint64_t localNumAssignedFragments{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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 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] &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 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 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 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 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] &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] 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] &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 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 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 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 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] &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] 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] 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 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 _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 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 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 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 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] 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 std::pair emplace_impl(std::size_t ibucket, typename array_bucket::const_iterator end_of_bucket, ^ 37 warnings generated. [ 89%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] 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] 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 && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: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] 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] 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] 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] 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] 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] 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] 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] 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] #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] 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] 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: /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] [&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] 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 std::mutex ffMutex_; ^ /usr/include/c++/v1/__mutex_base:40:5: note: 'mutex' has been explicitly marked deleted here mutex(const mutex&) = delete; ^ 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:17:29: warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted] 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 std::mutex ffMutex_; ^ /usr/include/c++/v1/__mutex_base:41:12: note: 'operator=' has been explicitly marked deleted here mutex& operator=(const mutex&) = 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] double auxProbSum{0.0}; ^ /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] uint64_t localNumAssignedFragments{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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 edges[source].insert(sink); ^ 27 warnings generated. [ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: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] 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] 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] 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] 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] 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] 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] 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] void serialize(Archive& ar, const unsigned int version) { ^ 8 warnings generated. [ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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 && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: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] 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] 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] 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] 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] 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] 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] 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] 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: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] 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] 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: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] #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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 edges[source].insert(sink); ^ 22 warnings generated. [ 93%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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] #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: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] 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] 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] 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] 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] 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] 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] 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] void serialize(Archive& ar, const unsigned int version) { ^ 9 warnings generated. [ 94%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: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] 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] 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] 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] 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] 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] 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] void bits(unsigned b) { } // NOOP ^ 7 warnings generated. [ 95%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] 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: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] 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] 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] 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] 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] 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] 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] 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] 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: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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 gcBitArray_[i] = 1; ^ 16 warnings generated. [ 96%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: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] 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] 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] 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] 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] 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] 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] 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] 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] 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 transitionProbsLeft_[i] = std::move(AtomicMatrix( ^~~~~~~~~~ /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] 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 transitionProbsRight_[i] = std::move(AtomicMatrix( ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:96:33: warning: unused parameter 'primary' [-Wunused-parameter] 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] 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] 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 gcBitArray_[i] = 1; ^ 20 warnings generated. [ 96%] Building CXX object src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 gcBitArray_[i] = 1; ^ 19 warnings generated. [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: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] 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] 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] 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] 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] 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] 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] 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] 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 gcBitArray_[i] = 1; ^ 15 warnings generated. [ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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: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] 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] 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] 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] 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] 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] 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] 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] 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: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] 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] 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: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] #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] 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 std::mutex ffMutex_; ^ /usr/include/c++/v1/__mutex_base:40:5: note: 'mutex' has been explicitly marked deleted here mutex(const mutex&) = delete; ^ 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:17:29: warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted] 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 std::mutex ffMutex_; ^ /usr/include/c++/v1/__mutex_base:41:12: note: 'operator=' has been explicitly marked deleted here mutex& operator=(const mutex&) = delete; ^ /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] 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] 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 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 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 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 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 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] 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 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 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 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 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 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 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] 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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) 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 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 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 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, 0>' requested here 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 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, Eigen::internal::Dense2Dense>::run' requested here 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 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 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 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] 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 ? 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 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 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 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] 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 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 _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 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 _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 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 edges[source].insert(sink); ^ 25 warnings generated. [ 99%] Building CXX object src/CMakeFiles/salmon.dir/BAMUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /ccache/libexec/ccache/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -DTBB_USE_DEBUG -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 -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -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 -g -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -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 /ccache/libexec/ccache/c++ -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -flto=thin -lpthread -fstack-protector-strong 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.12.11 /usr/local/lib/libtbbmalloc.so.2.11 -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_2 ===> Generating temporary packing list install -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=2024-04-05T15:03:59+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=cf5d9b8b96' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for salmon-1.10.2_2 ===> Building salmon-1.10.2_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for salmon-1.10.2_2 build of biology/salmon | salmon-1.10.2_2 ended at Fri Apr 5 16:43:57 BST 2024 build time: 00:39:59