=>> Building biology/kallisto build started at Wed Mar 11 17:34:37 EDT 2026 port directory: /usr/ports/biology/kallisto package name: kallisto-0.52.0,1 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1656 Mar 6 20:23 /usr/ports/biology/kallisto/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: 64ae45e8c91f Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-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/freebsd_14_4_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/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 kallisto-0.52.0,1: 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=/usr/local/bin/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=/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" --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=/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=" -lhdf5 -lhts -lz -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-- PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=14.4 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--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---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 ===> kallisto-0.52.0,1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> kallisto-0.52.0,1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of kallisto-0.52.0,1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 => pachterlab-kallisto-v0.52.0_GH0.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.52.0?dummy=/pachterlab-kallisto-v0.52.0_GH0.tar.gz fetch: https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.52.0?dummy=/pachterlab-kallisto-v0.52.0_GH0.tar.gz: size unknown fetch: https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.52.0?dummy=/pachterlab-kallisto-v0.52.0_GH0.tar.gz: size of remote file is not known pachterlab-kallisto-v0.52.0_GH0.tar.gz 5821 kB 121 kBps 48s ===> Fetching all distfiles required by kallisto-0.52.0,1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by kallisto-0.52.0,1 for building => SHA256 Checksum OK for pachterlab-kallisto-v0.52.0_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-0.52.0,1 for building ===> Extracting for kallisto-0.52.0,1 => SHA256 Checksum OK for pachterlab-kallisto-v0.52.0_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 kallisto-0.52.0,1 ===> Applying FreeBSD patches for kallisto-0.52.0,1 from /usr/ports/biology/kallisto/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> kallisto-0.52.0,1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.10_1.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.10_1... [pkg.DaveG.ca] `-- Installing expat-2.7.4... [pkg.DaveG.ca] `-- Extracting expat-2.7.4: .......... done [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Installing libunistring-1.4.2... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.2: .......... done [pkg.DaveG.ca] `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.52.0... [pkg.DaveG.ca] `-- Extracting libuv-1.52.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.6... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] `-- Extracting rhash-1.4.6: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.10_1: .......... done ===> kallisto-0.52.0,1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of kallisto-0.52.0,1 ===> kallisto-0.52.0,1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> kallisto-0.52.0,1 depends on package: gmake>=4.4.1 - found ===> Returning to build of kallisto-0.52.0,1 ===> kallisto-0.52.0,1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] 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. ===> kallisto-0.52.0,1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of kallisto-0.52.0,1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> kallisto-0.52.0,1 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.12.2_2,1.pkg [pkg.DaveG.ca] Installing hdf5-1.12.2_2,1... [pkg.DaveG.ca] `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc14-14.2.0_4: .......... done create symlink for gcc14 create symlink for gcc14 (world) create symlink for g++14 create symlink for g++14 (world) create symlink for cpp14 create symlink for cpp14 (world) [pkg.DaveG.ca] `-- Installing libaec-1.1.4... [pkg.DaveG.ca] `-- Extracting libaec-1.1.4: .......... done [pkg.DaveG.ca] Extracting hdf5-1.12.2_2,1: .......... done ===== Message from gcc14-14.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> kallisto-0.52.0,1 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of kallisto-0.52.0,1 ===> kallisto-0.52.0,1 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) ===> kallisto-0.52.0,1 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.22.pkg [pkg.DaveG.ca] Installing htslib-1.22... [pkg.DaveG.ca] `-- Installing curl-8.17.0... [pkg.DaveG.ca] | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.17.0: .......... done [pkg.DaveG.ca] `-- Installing libdeflate-1.25... [pkg.DaveG.ca] `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] Extracting htslib-1.22: .......... done ===> kallisto-0.52.0,1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of kallisto-0.52.0,1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for kallisto-0.52.0,1 /usr/bin/sed -i.bak -e "s|-Wno-return-type|& -I/usr/local/include|g" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/CMakeLists.txt ===> 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 < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is Clang 19.1.7 -- The CXX compiler identification is Clang 19.1.7 -- 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 -- 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 ZLIB: /usr/lib/libz.so (found version "1.3.1") -- Configuring done (2.4s) -- 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 -- 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-0.52.0,1 /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0 -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 /usr/local/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' /usr/local/bin/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-0.52.0 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0 /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' /usr/local/bin/gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' [ 2%] Creating directories for 'bifrost' /usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/tmp/bifrost-mkdirs.cmake /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/bifrost-stamp/bifrost-mkdir [ 4%] 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-0.52.0/ext/bifrost/src/bifrost-stamp/bifrost-download [ 7%] 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-0.52.0/ext/bifrost/src/bifrost-stamp/bifrost-update [ 9%] 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-0.52.0/ext/bifrost/src/bifrost-stamp/bifrost-patch [ 11%] Performing configure step for 'bifrost' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost && mkdir -p build && cd build && cmake .. -DMAX_KMER_SIZE=32 -DCMAKE_INSTALL_PREFIX= "-DCMAKE_CXX_FLAGS=-Wno-return-type -I/usr/local/include" CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is Clang 19.1.7 -- The CXX compiler identification is Clang 19.1.7 -- 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 -- 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 "1.3.1") -- Configuring done (1.9s) -- Generating done (0.0s) -- Build files have been written to: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/bifrost-stamp/bifrost-configure [ 14%] Performing build step for 'bifrost' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost && cd build && gmake gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build' /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost -B/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/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-0.52.0/ext/bifrost/build/CMakeFiles /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build//CMakeFiles/progress.marks gmake -f CMakeFiles/Makefile2 all gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/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-0.52.0/ext/bifrost/build' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color=" gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/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-0.52.0/ext/bifrost/build' [ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -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 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/Bifrost.cpp [ 6%] Building CXX object src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_static.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/BitContainer.cpp [ 9%] Building CXX object src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/BlockedBloomFilter.cpp [ 12%] Building CXX object src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o -MF CMakeFiles/bifrost_static.dir/ColorSet.cpp.o.d -o CMakeFiles/bifrost_static.dir/ColorSet.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/ColorSet.cpp [ 15%] Building CXX object src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o -MF CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o.d -o CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/CompressedCoverage.cpp [ 18%] Building CXX object src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o -MF CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o.d -o CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/CompressedSequence.cpp [ 21%] Building CXX object src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o -MF CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o.d -o CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/FASTX_Parser.cpp [ 25%] Building CXX object src/CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o -MF CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o.d -o CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/GFA_Parser.cpp [ 28%] Building CXX object src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o -MF CMakeFiles/bifrost_static.dir/Kmer.cpp.o.d -o CMakeFiles/bifrost_static.dir/Kmer.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/Kmer.cpp [ 31%] Building CXX object src/CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o -MF CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o.d -o CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/KmerIterator.cpp [ 34%] Building CXX object src/CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o -MF CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o.d -o CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/MinimizerIndex.cpp [ 37%] Building CXX object src/CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o -MF CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o.d -o CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/TinyBitmap.cpp [ 40%] Building CXX object src/CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o -MF CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o.d -o CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/UnitigMap.cpp [ 43%] Building C object src/CMakeFiles/bifrost_static.dir/roaring.c.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/cc -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c11 -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/roaring.c.o -MF CMakeFiles/bifrost_static.dir/roaring.c.o.d -o CMakeFiles/bifrost_static.dir/roaring.c.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/roaring.c [ 46%] Linking CXX static library libbifrost.a cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/bin/cmake -P CMakeFiles/bifrost_static.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/bifrost_static.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libbifrost.a CMakeFiles/bifrost_static.dir/Bifrost.cpp.o CMakeFiles/bifrost_static.dir/BitContainer.cpp.o CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o CMakeFiles/bifrost_static.dir/ColorSet.cpp.o CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o 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-0.52.0/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-0.52.0/ext/bifrost/build' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src/CMakeFiles/bifrost_dynamic.dir/DependInfo.cmake "--color=" gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build' gmake -f src/CMakeFiles/bifrost_dynamic.dir/build.make src/CMakeFiles/bifrost_dynamic.dir/build gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build' [ 50%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/Bifrost.cpp [ 53%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/BitContainer.cpp [ 56%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/BlockedBloomFilter.cpp [ 59%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/ColorSet.cpp [ 62%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/CompressedCoverage.cpp [ 65%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/CompressedSequence.cpp [ 68%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/FASTX_Parser.cpp [ 71%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/GFA_Parser.cpp [ 75%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/Kmer.cpp [ 78%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/KmerIterator.cpp [ 81%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/MinimizerIndex.cpp [ 84%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/TinyBitmap.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/TinyBitmap.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/TinyBitmap.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/TinyBitmap.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/TinyBitmap.cpp [ 87%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/UnitigMap.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/UnitigMap.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/UnitigMap.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/UnitigMap.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/UnitigMap.cpp [ 90%] Building C object src/CMakeFiles/bifrost_dynamic.dir/roaring.c.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/cc -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c11 -O3 -DNDEBUG -fPIC -O2 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/roaring.c.o -MF CMakeFiles/bifrost_dynamic.dir/roaring.c.o.d -o CMakeFiles/bifrost_dynamic.dir/roaring.c.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/roaring.c [ 93%] Linking CXX shared library libbifrost.so cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/bifrost_dynamic.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -Xlinker --dependency-file=CMakeFiles/bifrost_dynamic.dir/link.d -lhdf5 -lhts -lz -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 directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build' [ 93%] Built target bifrost_dynamic gmake -f src/CMakeFiles/Bifrost.dir/build.make src/CMakeFiles/Bifrost.dir/depend gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src/CMakeFiles/Bifrost.dir/DependInfo.cmake "--color=" gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build' gmake -f src/CMakeFiles/Bifrost.dir/build.make src/CMakeFiles/Bifrost.dir/build gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build' [ 96%] Building CXX object src/CMakeFiles/Bifrost.dir/Bifrost.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/Bifrost.dir/Bifrost.cpp.o -MF CMakeFiles/Bifrost.dir/Bifrost.cpp.o.d -o CMakeFiles/Bifrost.dir/Bifrost.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/Bifrost.cpp [100%] Linking CXX executable Bifrost cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Bifrost.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -Wno-return-type -I/usr/local/include -std=c++11 -Wno-unqualified-std-cast-call -O3 -DNDEBUG -lhdf5 -lhts -lz -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/Bifrost.dir/link.d CMakeFiles/Bifrost.dir/Bifrost.cpp.o -o Bifrost -Wl,-rpath,/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src: libbifrost.so -lpthread -lz gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build' [100%] Built target Bifrost gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build' /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/CMakeFiles 0 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/bifrost-stamp/bifrost-build [ 16%] No install step for 'bifrost' cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost && /usr/local/bin/cmake -E echo_append cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src/bifrost-stamp/bifrost-install [ 19%] 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-0.52.0/ext/bifrost/src/bifrost-stamp/bifrost-done gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' [ 19%] Built target bifrost /usr/local/bin/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-0.52.0 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/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' /usr/local/bin/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' [ 21%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-0.52.0/src/BUSData.cpp [ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSTools.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/BUSTools.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/BUSTools.cpp:3: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/BUSTools.h:6: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/MinCollector.h:4: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 26%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-0.52.0/src/Bootstrap.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Bootstrap.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Bootstrap.h:8: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.h:13: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 28%] Building CXX object src/CMakeFiles/kallisto_core.dir/Fusion.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Fusion.cpp.o -MF CMakeFiles/kallisto_core.dir/Fusion.cpp.o.d -o CMakeFiles/kallisto_core.dir/Fusion.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Fusion.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Fusion.cpp:4: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/ProcessReads.h:16: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 30%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-0.52.0/src/GeneModel.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/GeneModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/GeneModel.h:9: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -MF CMakeFiles/kallisto_core.dir/H5Writer.cpp.o.d -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/H5Writer.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/H5Writer.cpp:2: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/H5Writer.h:5: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/EMAlgorithm.h:4: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 35%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -MF CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o.d -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.h:13: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/robin_hood.h:1445:33: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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__) | ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/robin_hood.h:1605:13: note: in instantiation of member function 'robin_hood::detail::Table>::cloneData' requested here 1605 | cloneData(o); | ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.cpp:716:7: note: in instantiation of member function 'robin_hood::detail::Table>::Table' requested here 716 | kmers; // copy; kmers_special will be the ones we store as-is (i.e. not flanking); these are | ^ 2 warnings generated. [ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -MF CMakeFiles/kallisto_core.dir/MinCollector.cpp.o.d -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/MinCollector.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/MinCollector.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/MinCollector.h:4: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 40%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -MF CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o.d -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/PlaintextWriter.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/PlaintextWriter.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/PlaintextWriter.h:12: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-0.52.0/src/ProcessReads.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/ProcessReads.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/ProcessReads.h:16: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 45%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-0.52.0/src/PseudoBam.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/PseudoBam.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/common.cpp.o -MF CMakeFiles/kallisto_core.dir/common.cpp.o.d -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.cpp:3: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 50%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-0.52.0/src/h5utils.cpp [ 52%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-0.52.0/src/hash.cpp [ 54%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-0.52.0/src/main.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/main.cpp:17: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Bootstrap.h:8: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.h:13: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-0.52.0/src/weights.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/weights.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/weights.h:4: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.h:13: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 59%] 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/Fusion.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' [ 59%] Built target kallisto_core /usr/local/bin/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-0.52.0 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/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' /usr/local/bin/gmake -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' [ 61%] Building CXX object src/CMakeFiles/kallisto.dir/main.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -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-0.52.0/src/main.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/main.cpp:17: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Bootstrap.h:8: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.h:13: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 64%] Building CXX object src/CMakeFiles/kallisto.dir/BUSData.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/BUSData.cpp.o -MF CMakeFiles/kallisto.dir/BUSData.cpp.o.d -o CMakeFiles/kallisto.dir/BUSData.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/BUSData.cpp [ 66%] Building CXX object src/CMakeFiles/kallisto.dir/BUSTools.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/BUSTools.cpp.o -MF CMakeFiles/kallisto.dir/BUSTools.cpp.o.d -o CMakeFiles/kallisto.dir/BUSTools.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/BUSTools.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/BUSTools.cpp:3: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/BUSTools.h:6: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/MinCollector.h:4: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 69%] Building CXX object src/CMakeFiles/kallisto.dir/Bootstrap.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/Bootstrap.cpp.o -MF CMakeFiles/kallisto.dir/Bootstrap.cpp.o.d -o CMakeFiles/kallisto.dir/Bootstrap.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Bootstrap.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Bootstrap.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Bootstrap.h:8: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.h:13: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 71%] Building CXX object src/CMakeFiles/kallisto.dir/Fusion.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/Fusion.cpp.o -MF CMakeFiles/kallisto.dir/Fusion.cpp.o.d -o CMakeFiles/kallisto.dir/Fusion.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Fusion.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/Fusion.cpp:4: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/ProcessReads.h:16: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 73%] Building CXX object src/CMakeFiles/kallisto.dir/GeneModel.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/GeneModel.cpp.o -MF CMakeFiles/kallisto.dir/GeneModel.cpp.o.d -o CMakeFiles/kallisto.dir/GeneModel.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/GeneModel.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/GeneModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/GeneModel.h:9: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 76%] Building CXX object src/CMakeFiles/kallisto.dir/H5Writer.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/H5Writer.cpp.o -MF CMakeFiles/kallisto.dir/H5Writer.cpp.o.d -o CMakeFiles/kallisto.dir/H5Writer.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/H5Writer.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/H5Writer.cpp:2: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/H5Writer.h:5: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/EMAlgorithm.h:4: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 78%] Building CXX object src/CMakeFiles/kallisto.dir/KmerIndex.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/KmerIndex.cpp.o -MF CMakeFiles/kallisto.dir/KmerIndex.cpp.o.d -o CMakeFiles/kallisto.dir/KmerIndex.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.h:13: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/robin_hood.h:1445:33: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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__) | ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/robin_hood.h:1605:13: note: in instantiation of member function 'robin_hood::detail::Table>::cloneData' requested here 1605 | cloneData(o); | ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.cpp:716:7: note: in instantiation of member function 'robin_hood::detail::Table>::Table' requested here 716 | kmers; // copy; kmers_special will be the ones we store as-is (i.e. not flanking); these are | ^ 2 warnings generated. [ 80%] Building CXX object src/CMakeFiles/kallisto.dir/MinCollector.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/MinCollector.cpp.o -MF CMakeFiles/kallisto.dir/MinCollector.cpp.o.d -o CMakeFiles/kallisto.dir/MinCollector.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/MinCollector.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/MinCollector.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/MinCollector.h:4: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 83%] Building CXX object src/CMakeFiles/kallisto.dir/PlaintextWriter.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/PlaintextWriter.cpp.o -MF CMakeFiles/kallisto.dir/PlaintextWriter.cpp.o.d -o CMakeFiles/kallisto.dir/PlaintextWriter.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/PlaintextWriter.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/PlaintextWriter.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/PlaintextWriter.h:12: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 85%] Building CXX object src/CMakeFiles/kallisto.dir/ProcessReads.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/ProcessReads.cpp.o -MF CMakeFiles/kallisto.dir/ProcessReads.cpp.o.d -o CMakeFiles/kallisto.dir/ProcessReads.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/ProcessReads.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/ProcessReads.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/ProcessReads.h:16: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 88%] Building CXX object src/CMakeFiles/kallisto.dir/PseudoBam.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/PseudoBam.cpp.o -MF CMakeFiles/kallisto.dir/PseudoBam.cpp.o.d -o CMakeFiles/kallisto.dir/PseudoBam.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/PseudoBam.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/PseudoBam.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 90%] Building CXX object src/CMakeFiles/kallisto.dir/common.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/common.cpp.o -MF CMakeFiles/kallisto.dir/common.cpp.o.d -o CMakeFiles/kallisto.dir/common.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.cpp:3: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [ 92%] Building CXX object src/CMakeFiles/kallisto.dir/h5utils.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/h5utils.cpp.o -MF CMakeFiles/kallisto.dir/h5utils.cpp.o.d -o CMakeFiles/kallisto.dir/h5utils.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/h5utils.cpp [ 95%] Building CXX object src/CMakeFiles/kallisto.dir/hash.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/hash.cpp.o -MF CMakeFiles/kallisto.dir/hash.cpp.o.d -o CMakeFiles/kallisto.dir/hash.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/hash.cpp [ 97%] Building CXX object src/CMakeFiles/kallisto.dir/weights.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/libexec/ccache/c++ -DMAX_KMER_SIZE=32 -DUSE_HDF5=ON -I/usr/local/htslib -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/src -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/weights.cpp.o -MF CMakeFiles/kallisto.dir/weights.cpp.o.d -o CMakeFiles/kallisto.dir/weights.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/weights.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/weights.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/weights.h:4: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/KmerIndex.h:13: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/common.h:20: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/src/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/kallisto/work/kallisto-0.52.0/src/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__) | ^ 1 warning generated. [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 /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wno-unqualified-std-cast-call -isystem /usr/local/include -DNDEBUG -lhdf5 -lhts -lz -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/kallisto.dir/link.d CMakeFiles/kallisto.dir/main.cpp.o CMakeFiles/kallisto.dir/BUSData.cpp.o CMakeFiles/kallisto.dir/BUSTools.cpp.o CMakeFiles/kallisto.dir/Bootstrap.cpp.o CMakeFiles/kallisto.dir/Fusion.cpp.o CMakeFiles/kallisto.dir/GeneModel.cpp.o CMakeFiles/kallisto.dir/H5Writer.cpp.o CMakeFiles/kallisto.dir/KmerIndex.cpp.o CMakeFiles/kallisto.dir/MinCollector.cpp.o CMakeFiles/kallisto.dir/PlaintextWriter.cpp.o CMakeFiles/kallisto.dir/ProcessReads.cpp.o CMakeFiles/kallisto.dir/PseudoBam.cpp.o CMakeFiles/kallisto.dir/common.cpp.o CMakeFiles/kallisto.dir/h5utils.cpp.o CMakeFiles/kallisto.dir/hash.cpp.o CMakeFiles/kallisto.dir/weights.cpp.o -o kallisto libkallisto_core.a -lpthread /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/ext/bifrost/build/src/libbifrost.a -DMAX_KMER_SIZE=32 libkallisto_core.a -lz -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-0.52.0,1 ===> Generating temporary packing list /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0 -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 /usr/local/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' /usr/local/bin/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-0.52.0 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0 /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' /usr/local/bin/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' [ 19%] Built target bifrost /usr/local/bin/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-0.52.0 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/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' /usr/local/bin/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' [ 59%] Built target kallisto_core /usr/local/bin/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-0.52.0 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.52.0/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' /usr/local/bin/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 /usr/local/bin/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 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-0.52.0/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=2026-03-11T21:34:37+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=64ae45e8c91f' '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 kallisto-0.52.0,1 ===> Building kallisto-0.52.0,1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for kallisto-0.52.0,1 build of biology/kallisto | kallisto-0.52.0,1 ended at Wed Mar 11 17:45:48 EDT 2026 build time: 00:11:12