=>> Building biology/kallisto build started at Fri Mar 29 08:07:11 GMT 2024 port directory: /usr/ports/biology/kallisto package name: kallisto-0.50.1,1 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 1369 Nov 5 07:03 /usr/ports/biology/kallisto/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 8a2deaeb09 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 06 ---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/06/.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--- ===> The following configuration options are available for kallisto-0.50.1,1: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---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/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/kallisto/work/.cache HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/kallisto/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/kallisto/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/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/kallisto/work/.cache HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/kallisto/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/kallisto/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lhts -lz -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 " CCACHE_DIR="/root/.ccache" 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-- PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/kallisto" EXAMPLESDIR="share/examples/kallisto" DATADIR="share/kallisto" WWWDIR="www/kallisto" ETCDIR="etc/kallisto" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/kallisto DOCSDIR=/usr/local/share/doc/kallisto EXAMPLESDIR=/usr/local/share/examples/kallisto WWWDIR=/usr/local/www/kallisto ETCDIR=/usr/local/etc/kallisto --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 ===> kallisto-0.50.1,1 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 ===> kallisto-0.50.1,1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of kallisto-0.50.1,1 =========================================================================== =================================================== ===== 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 kallisto-0.50.1,1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by kallisto-0.50.1,1 for building => SHA256 Checksum OK for pachterlab-kallisto-v0.50.1_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 kallisto-0.50.1,1 for building ===> Extracting for kallisto-0.50.1,1 => SHA256 Checksum OK for pachterlab-kallisto-v0.50.1_GH0.tar.gz. /bin/rm -f -rf /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/htslib =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for kallisto-0.50.1,1 ===> Applying FreeBSD patches for kallisto-0.50.1,1 from /usr/ports/biology/kallisto/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> kallisto-0.50.1,1 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] | `-- 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 rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.28.3: .......... done ===> kallisto-0.50.1,1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of kallisto-0.50.1,1 ===> kallisto-0.50.1,1 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 ===> kallisto-0.50.1,1 depends on package: gmake>=4.4.1 - found ===> Returning to build of kallisto-0.50.1,1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> kallisto-0.50.1,1 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.12.2_2,1.pkg [pkg-builder.dan.net.uk] Installing hdf5-1.12.2_2,1... [pkg-builder.dan.net.uk] Extracting hdf5-1.12.2_2,1: .......... done ===> kallisto-0.50.1,1 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of kallisto-0.50.1,1 ===> kallisto-0.50.1,1 depends on shared library: libsz.so - not found ===> Installing existing package /packages/All/libaec-1.1.2.pkg [pkg-builder.dan.net.uk] Installing libaec-1.1.2... [pkg-builder.dan.net.uk] Extracting libaec-1.1.2: .......... done ===> kallisto-0.50.1,1 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) ===> Returning to build of kallisto-0.50.1,1 ===> kallisto-0.50.1,1 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.17_1.pkg [pkg-builder.dan.net.uk] Installing htslib-1.17_1... [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 [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.19... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.19: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.17_1: .......... done ===> kallisto-0.50.1,1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of kallisto-0.50.1,1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for kallisto-0.50.1,1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/kallisto/work/.build CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- 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 -- Performing Test COMPILER_SUPPORTS_CXX17 -- Performing Test COMPILER_SUPPORTS_CXX17 - Success shared build -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found HDF5: hdf5-shared (found version "1.12.2") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.13") -- Configuring done (55.7s) -- Generating done (0.7s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /wrkdirs/usr/ports/biology/kallisto/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for kallisto-0.50.1,1 /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1 -B/wrkdirs/usr/ports/biology/kallisto/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/kallisto/work/.build//CMakeFiles/progress.marks gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' cd /wrkdirs/usr/ports/biology/kallisto/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1 /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles/bifrost.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' [ 3%] Creating directories for 'bifrost' /usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/tmp/bifrost-mkdirs.cmake /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-mkdir [ 7%] No download step for 'bifrost' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-download [ 11%] No update step for 'bifrost' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-update [ 15%] No patch step for 'bifrost' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-patch [ 19%] Performing configure step for 'bifrost' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost && mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX= -DCMAKE_CXX_FLAGS=-Wno-return-type CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- 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 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE Compilation architecture: Build type: Release Maximum k-mer size: 31 Maximum g-mer size: 31 -- Found ZLIB: /usr/lib/libz.so (found version "1.2.13") -- Configuring done (43.7s) -- Generating done (2.1s) -- Build files have been written to: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-configure [ 23%] Performing build step for 'bifrost' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost && cd build && gmake gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build' /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost -B/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/CMakeFiles /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build//CMakeFiles/progress.marks gmake -f CMakeFiles/Makefile2 all gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build' gmake -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/depend gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color=" gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build' gmake -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/build gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build' [ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src && /ccache/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -Wno-return-type -std=c++11 -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c 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CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o CMakeFiles/bifrost_static.dir/Kmer.cpp.o CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o CMakeFiles/bifrost_static.dir/roaring.c.o /usr/bin/llvm-ranlib libbifrost.a gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build' [ 46%] Built target bifrost_static gmake -f src/CMakeFiles/bifrost_dynamic.dir/build.make src/CMakeFiles/bifrost_dynamic.dir/depend gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost 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/usr/local/bin/cmake -E cmake_link_script CMakeFiles/bifrost_dynamic.dir/link.txt --verbose=1 /ccache/libexec/ccache/c++ -fPIC -Wno-return-type -std=c++11 -O3 -DNDEBUG -lhts -lz -fstack-protector-strong -L/usr/local/lib -shared -Wl,-soname,libbifrost.so -o libbifrost.so CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o CMakeFiles/bifrost_dynamic.dir/TinyBitmap.cpp.o CMakeFiles/bifrost_dynamic.dir/UnitigMap.cpp.o CMakeFiles/bifrost_dynamic.dir/roaring.c.o -lpthread -lz gmake[5]: Leaving 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-O3 -DNDEBUG -lhts -lz -fstack-protector-strong -L/usr/local/lib CMakeFiles/Bifrost.dir/Bifrost.cpp.o -o Bifrost -Wl,-rpath,/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src: libbifrost.so -lpthread -lz gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build' [100%] Built target Bifrost gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build' /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/CMakeFiles 0 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-build [ 26%] No install step for 'bifrost' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost && /usr/local/bin/cmake -E echo_append cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-install [ 30%] Completed 'bifrost' /usr/local/bin/cmake -E make_directory /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles/bifrost-complete /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-done gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' [ 30%] Built target bifrost gmake -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' cd 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-I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSData.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/BUSData.cpp [ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /ccache/libexec/ccache/c++ -DH5_BUILT_AS_DYNAMIC_LIB -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src 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/usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/Bootstrap.cpp [ 46%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /ccache/libexec/ccache/c++ -DH5_BUILT_AS_DYNAMIC_LIB -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -MF CMakeFiles/kallisto_core.dir/GeneModel.cpp.o.d -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/GeneModel.cpp [ 50%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /ccache/libexec/ccache/c++ -DH5_BUILT_AS_DYNAMIC_LIB -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD 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/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/PlaintextWriter.cpp [ 65%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /ccache/libexec/ccache/c++ -DH5_BUILT_AS_DYNAMIC_LIB -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -MF CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o.d -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/ProcessReads.cpp [ 69%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /ccache/libexec/ccache/c++ -DH5_BUILT_AS_DYNAMIC_LIB -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -MF CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o.d -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/PseudoBam.cpp [ 73%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o cd 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-DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o -MF CMakeFiles/kallisto_core.dir/h5utils.cpp.o.d -o CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/h5utils.cpp [ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /ccache/libexec/ccache/c++ -DH5_BUILT_AS_DYNAMIC_LIB -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/hash.cpp.o -MF CMakeFiles/kallisto_core.dir/hash.cpp.o.d -o CMakeFiles/kallisto_core.dir/hash.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/hash.cpp [ 84%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /ccache/libexec/ccache/c++ -DH5_BUILT_AS_DYNAMIC_LIB -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/main.cpp.o -MF CMakeFiles/kallisto_core.dir/main.cpp.o.d -o CMakeFiles/kallisto_core.dir/main.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/main.cpp [ 88%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /ccache/libexec/ccache/c++ -DH5_BUILT_AS_DYNAMIC_LIB -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/weights.cpp.o -MF CMakeFiles/kallisto_core.dir/weights.cpp.o.d -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/weights.cpp [ 92%] Linking CXX static library libkallisto_core.a cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/bin/cmake -P CMakeFiles/kallisto_core.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/kallisto_core.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libkallisto_core.a CMakeFiles/kallisto_core.dir/BUSData.cpp.o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o CMakeFiles/kallisto_core.dir/common.cpp.o CMakeFiles/kallisto_core.dir/h5utils.cpp.o CMakeFiles/kallisto_core.dir/hash.cpp.o CMakeFiles/kallisto_core.dir/main.cpp.o CMakeFiles/kallisto_core.dir/weights.cpp.o /usr/bin/llvm-ranlib libkallisto_core.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' [ 92%] Built target kallisto_core gmake -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' cd /wrkdirs/usr/ports/biology/kallisto/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1 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/usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/main.cpp.o -MF CMakeFiles/kallisto.dir/main.cpp.o.d -o CMakeFiles/kallisto.dir/main.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src/main.cpp [100%] Linking CXX executable kallisto cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/kallisto.dir/link.txt --verbose=1 /ccache/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -lhts -lz -fstack-protector-strong -L/usr/local/lib CMakeFiles/kallisto.dir/main.cpp.o -o kallisto -Wl,-rpath,/usr/local/lib: libkallisto_core.a -lpthread -lhts /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src/libbifrost.a libkallisto_core.a -lz /usr/local/lib/libhdf5.so.200.2.0 -lrt gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' [100%] Built target kallisto gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/kallisto/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 kallisto-0.50.1,1 ===> Generating temporary packing list /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1 -B/wrkdirs/usr/ports/biology/kallisto/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/kallisto/work/.build//CMakeFiles/progress.marks gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' cd /wrkdirs/usr/ports/biology/kallisto/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1 /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles/bifrost.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake[2]: Nothing to be done for 'CMakeFiles/bifrost.dir/build'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' [ 30%] Built target bifrost gmake -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' cd /wrkdirs/usr/ports/biology/kallisto/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build/src /wrkdirs/usr/ports/biology/kallisto/work/.build/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake[2]: Nothing to be done for 'src/CMakeFiles/kallisto_core.dir/build'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' [ 92%] Built target kallisto_core gmake -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' cd /wrkdirs/usr/ports/biology/kallisto/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/src /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build/src /wrkdirs/usr/ports/biology/kallisto/work/.build/src/CMakeFiles/kallisto.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake[2]: Nothing to be done for 'src/CMakeFiles/kallisto.dir/build'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' [100%] Built target kallisto gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles 0 gmake -f CMakeFiles/Makefile2 preinstall gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake[1]: Nothing to be done for 'preinstall'. gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/kallisto/work/stage/usr/local/bin/kallisto -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/kallisto/work/stage/usr/local/bin/kallisto" to "/usr/local/lib" install -m 555 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-test /wrkdirs/usr/ports/biology/kallisto/work/stage/usr/local/bin cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.1/test && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/kallisto/work/stage/usr/local/share/examples/kallisto ====> 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=2024-03-29T08:07:11+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=8a2deaeb09' '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 kallisto-0.50.1,1 ===> Building kallisto-0.50.1,1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for kallisto-0.50.1,1 build of biology/kallisto | kallisto-0.50.1,1 ended at Fri Mar 29 08:19:14 GMT 2024 build time: 00:12:06