=>> Building biology/mashmap build started at Mon May 5 22:19:12 BST 2025 port directory: /usr/ports/biology/mashmap package name: mashmap-3.1.3 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 858 Dec 29 14:16 /usr/ports/biology/mashmap/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 01 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/01/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for mashmap-3.1.3: NATIVE=off: Use native optimization (-march=native) ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mashmap/work/.cache HOME=/wrkdirs/usr/ports/biology/mashmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mashmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mashmap/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mashmap/work/.cache HOME=/wrkdirs/usr/ports/biology/mashmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mashmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mashmap/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/mashmap/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/mashmap" EXAMPLESDIR="share/examples/mashmap" DATADIR="share/mashmap" WWWDIR="www/mashmap" ETCDIR="etc/mashmap" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mashmap DOCSDIR=/usr/local/share/doc/mashmap EXAMPLESDIR=/usr/local/share/examples/mashmap WWWDIR=/usr/local/www/mashmap ETCDIR=/usr/local/etc/mashmap --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mashmap-3.1.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> mashmap-3.1.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mashmap-3.1.3 =========================================================================== =================================================== ===== 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 mashmap-3.1.3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mashmap-3.1.3 for building => SHA256 Checksum OK for marbl-MashMap-v3.1.3_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 mashmap-3.1.3 for building ===> Extracting for mashmap-3.1.3 => SHA256 Checksum OK for marbl-MashMap-v3.1.3_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 mashmap-3.1.3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mashmap-3.1.3 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.6.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.31.6... [pkg-builder.dan.net.uk] `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.6_1... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.51.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.51.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.31.6: .......... done ===> mashmap-3.1.3 depends on file: /usr/local/bin/cmake - found ===> Returning to build of mashmap-3.1.3 ===> mashmap-3.1.3 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,4.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,4... [pkg-builder.dan.net.uk] `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,4: ..... done ===== Message from python311-3.11.12: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> mashmap-3.1.3 depends on executable: ninja - found ===> Returning to build of mashmap-3.1.3 ===> mashmap-3.1.3 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.3.0_1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.3.0_1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.3.0_1,1: .......... done ===> mashmap-3.1.3 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of mashmap-3.1.3 ===> mashmap-3.1.3 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> mashmap-3.1.3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of mashmap-3.1.3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mashmap-3.1.3 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [pkg-builder.dan.net.uk] Installing gsl-2.7.1_1... [pkg-builder.dan.net.uk] Extracting gsl-2.7.1_1: .......... done ===> mashmap-3.1.3 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of mashmap-3.1.3 ===> mashmap-3.1.3 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.21.pkg [pkg-builder.dan.net.uk] Installing htslib-1.21... [pkg-builder.dan.net.uk] `-- Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.21: .......... done ===> mashmap-3.1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of mashmap-3.1.3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for mashmap-3.1.3 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/mashmap/work/.build -- The C compiler identification is Clang 18.1.6 -- The CXX compiler identification is Clang 18.1.6 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_BUILD_TYPE: Release -- Found PkgConfig: /usr/local/bin/pkgconf (found version "2.3.0") -- Checking for module 'htslib' -- Found htslib, version 1.21 -- Configuring done (0.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/mashmap/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for mashmap-3.1.3 [ 16% 1/6] /usr/local/libexec/ccache/c++ -DUSE_HTSLIB -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap.dir/src/common/utils.cpp.o -MF CMakeFiles/mashmap.dir/src/common/utils.cpp.o.d -o CMakeFiles/mashmap.dir/src/common/utils.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/utils.cpp [ 33% 2/6] /usr/local/libexec/ccache/c++ -DUSE_HTSLIB -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -MF CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o.d -o CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/mash_map.cpp In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/mash_map.cpp:13: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/map_parameters.hpp:14: /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:560:40: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 560 | uint32_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:560:40: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:592:40: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 592 | uint64_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:592:40: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:624:41: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 624 | uint128_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:624:41: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1019:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1019 | char temp[length + 1]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1019:15: note: read of non-const variable 'length' is not allowed in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1017:9: note: declared here 1017 | int length = l[seed_no]; | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1054:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1054 | char temp[length - 1]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1054:15: note: read of non-const variable 'length' is not allowed in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1051:9: note: declared here 1051 | int length = l[seed_no]; | ^ In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/mash_map.cpp:15: /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/parseCmdArgs.hpp:601:24: warning: implicit conversion from 'type' (aka 'unsigned long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] 601 | = frac * std::numeric_limits::max(); | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/mash_map.cpp:17: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/computeMap.hpp:39: /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/robin-hood-hashing/robin_hood.h:1445:33: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 1445 | Cloner()(o, *this); | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/robin-hood-hashing/robin_hood.h:210:51: note: expanded from macro 'ROBIN_HOOD_IS_TRIVIALLY_COPYABLE' 210 | # define ROBIN_HOOD_IS_TRIVIALLY_COPYABLE(...) __has_trivial_copy(__VA_ARGS__) | ^ 7 warnings generated. [ 50% 3/6] : && /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -fstack-protector-strong -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/mashmap.dir/link.d CMakeFiles/mashmap.dir/src/common/utils.cpp.o CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -o bin/mashmap -lgsl -lgslcblas -lm -lpthread -lz /usr/local/lib/libhts.so && : [ 66% 4/6] /usr/local/libexec/ccache/c++ -DUSE_HTSLIB -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o -MF CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o.d -o CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/utils.cpp [ 83% 5/6] /usr/local/libexec/ccache/c++ -DUSE_HTSLIB -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -MF CMakeFiles/mashmap-align.dir/src/align/align.cpp.o.d -o CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/align/align.cpp In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/align/align.cpp:18: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/align/include/parseCmdArgs.hpp:16: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/parseCmdArgs.hpp:16: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/map_parameters.hpp:14: /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:560:40: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 560 | uint32_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:560:40: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:592:40: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 592 | uint64_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:592:40: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:624:41: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 624 | uint128_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:624:41: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1019:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1019 | char temp[length + 1]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1019:15: note: read of non-const variable 'length' is not allowed in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1017:9: note: declared here 1017 | int length = l[seed_no]; | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1054:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1054 | char temp[length - 1]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1054:15: note: read of non-const variable 'length' is not allowed in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1051:9: note: declared here 1051 | int length = l[seed_no]; | ^ In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/align/align.cpp:18: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/align/include/parseCmdArgs.hpp:16: /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/parseCmdArgs.hpp:601:24: warning: implicit conversion from 'type' (aka 'unsigned long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] 601 | = frac * std::numeric_limits::max(); | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 6 warnings generated. [100% 6/6] : && /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -fstack-protector-strong -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/mashmap-align.dir/link.d CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -o bin/mashmap-align -lgsl -lgslcblas -lm -lpthread -lz /usr/local/lib/libhts.so && : =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for mashmap-3.1.3 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/biology/mashmap/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/mashmap/work/stage/usr/local/bin/mashmap -- Installing: /wrkdirs/usr/ports/biology/mashmap/work/stage/usr/local/bin/mashmap-align ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-05-05T21:19:12+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for mashmap-3.1.3 ===> Building mashmap-3.1.3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for mashmap-3.1.3 build of biology/mashmap | mashmap-3.1.3 ended at Mon May 5 22:21:21 BST 2025 build time: 00:02:09