=>> Building biology/vcflib build started at Tue Mar 10 20:34:01 EDT 2026 port directory: /usr/ports/biology/vcflib package name: vcflib-1.0.13 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 2007 Jan 5 20:59 /usr/ports/biology/vcflib/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: 2b60f0ede764 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 04 ---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/04/.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 vcflib-1.0.13: ZIG=off: Include Zig language support ===> 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 PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcflib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcflib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcflib/work/.cache HOME=/wrkdirs/usr/ports/biology/vcflib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcflib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcflib/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/vcflib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcflib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcflib/work/.cache HOME=/wrkdirs/usr/ports/biology/vcflib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcflib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcflib/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=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- ZIG="@comment " NO_ZIG="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/vcflib" EXAMPLESDIR="share/examples/vcflib" DATADIR="share/vcflib" WWWDIR="www/vcflib" ETCDIR="etc/vcflib" --End PLIST_SUB-- --SUB_LIST-- ZIG="@comment " NO_ZIG="" PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vcflib DOCSDIR=/usr/local/share/doc/vcflib EXAMPLESDIR=/usr/local/share/examples/vcflib WWWDIR=/usr/local/www/vcflib ETCDIR=/usr/local/etc/vcflib --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 ===> vcflib-1.0.13 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 ===> vcflib-1.0.13 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcflib-1.0.13 =========================================================================== =================================================== ===== 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 vcflib-1.0.13 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vcflib-1.0.13 for building => SHA256 Checksum OK for ekg-vcflib-v1.0.13_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-df20dcc_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-56695e1_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-aa59377_GH0.tar.gz. => SHA256 Checksum OK for edawson-libVCFH-44b6580_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-e1f94ae_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-2610e25_GH0.tar.gz. => SHA256 Checksum OK for simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz. => SHA256 Checksum OK for vcflib-tabixpp-ae5cdf8_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 vcflib-1.0.13 for building ===> Extracting for vcflib-1.0.13 => SHA256 Checksum OK for ekg-vcflib-v1.0.13_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-df20dcc_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-56695e1_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-aa59377_GH0.tar.gz. => SHA256 Checksum OK for edawson-libVCFH-44b6580_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-e1f94ae_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-2610e25_GH0.tar.gz. => SHA256 Checksum OK for simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz. => SHA256 Checksum OK for vcflib-tabixpp-ae5cdf8_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 vcflib-1.0.13 ===> Applying FreeBSD patches for vcflib-1.0.13 from /usr/ports/biology/vcflib/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcflib-1.0.13 depends on package: pybind11>0 - not found ===> Installing existing package /packages/All/pybind11-3.0.1.pkg [pkg.DaveG.ca] Installing pybind11-3.0.1... [pkg.DaveG.ca] Extracting pybind11-3.0.1: .......... done ===> vcflib-1.0.13 depends on package: pybind11>0 - found ===> Returning to build of vcflib-1.0.13 ===> vcflib-1.0.13 depends on package: py311-pypandoc>=1.4 - not found ===> Installing existing package /packages/All/py311-pypandoc-1.14_1.pkg [pkg.DaveG.ca] Installing py311-pypandoc-1.14_1... [pkg.DaveG.ca] `-- Installing hs-pandoc-3.8.3... [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] `-- Extracting hs-pandoc-3.8.3: .......... done [pkg.DaveG.ca] `-- Installing python311-3.11.15... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.15: .......... done [pkg.DaveG.ca] Extracting py311-pypandoc-1.14_1: .......... done ===== Message from python311-3.11.15: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> vcflib-1.0.13 depends on package: py311-pypandoc>=1.4 - found ===> Returning to build of vcflib-1.0.13 ===> vcflib-1.0.13 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 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] `-- Extracting rhash-1.4.6: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.10_1: .......... done ===> vcflib-1.0.13 depends on file: /usr/local/bin/cmake - found ===> Returning to build of vcflib-1.0.13 ===> vcflib-1.0.13 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 ===> vcflib-1.0.13 depends on package: gmake>=4.4.1 - found ===> Returning to build of vcflib-1.0.13 ===> vcflib-1.0.13 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> vcflib-1.0.13 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of vcflib-1.0.13 ===> vcflib-1.0.13 depends on file: /usr/local/bin/python3.11 - found ===> vcflib-1.0.13 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. ===> vcflib-1.0.13 depends on file: /usr/local/bin/ccache - found ===> Returning to build of vcflib-1.0.13 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcflib-1.0.13 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] | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7_1: .......... 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 ===> vcflib-1.0.13 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of vcflib-1.0.13 ===> vcflib-1.0.13 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> vcflib-1.0.13 depends on shared library: libwfa2.so - not found ===> Installing existing package /packages/All/wfa2-lib-2.3.5.pkg [pkg.DaveG.ca] Installing wfa2-lib-2.3.5... [pkg.DaveG.ca] Extracting wfa2-lib-2.3.5: .......... done ===> vcflib-1.0.13 depends on shared library: libwfa2.so - found (/usr/local/lib/libwfa2.so) ===> Returning to build of vcflib-1.0.13 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for vcflib-1.0.13 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/vcflib/work/.build -- 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 -- Found PkgConfig: /usr/local/bin/pkgconf (found version "2.4.3") CMake Warning (dev) at /usr/local/share/cmake/pybind11/FindPythonLibsNew.cmake:101 (message): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning, or preferably upgrade to using FindPython, either by calling it explicitly before pybind11, or by setting PYBIND11_FINDPYTHON ON before pybind11. Call Stack (most recent call first): /usr/local/share/cmake/pybind11/pybind11Tools.cmake:44 (find_package) /usr/local/share/cmake/pybind11/pybind11Common.cmake:226 (include) /usr/local/share/cmake/pybind11/pybind11Config.cmake:257 (include) CMakeLists.txt:19 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/local/bin/python3.11 (found suitable version "3.11.15", minimum required is "3.8") -- Found PythonLibs: /usr/local/lib/libpython3.11.so -- Performing Test HAS_FLTO_THIN -- Performing Test HAS_FLTO_THIN - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/local/include (found version "3.0.1") -- Found BZip2: /usr/lib/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for lzma_auto_decoder in /usr/lib/liblzma.so -- Looking for lzma_auto_decoder in /usr/lib/liblzma.so - found -- Looking for lzma_easy_encoder in /usr/lib/liblzma.so -- Looking for lzma_easy_encoder in /usr/lib/liblzma.so - found -- Looking for lzma_lzma_preset in /usr/lib/liblzma.so -- Looking for lzma_lzma_preset in /usr/lib/liblzma.so - found -- Found LibLZMA: /usr/lib/liblzma.so (found version "5.8.2") -- Found ZLIB: /usr/lib/libz.so (found version "1.3.1") -- Found CURL: /usr/local/lib/libcurl.so (found version "8.17.0") -- -- Found OpenMP_C: -fopenmp=libomp (found version "5.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") -- Found OpenMP: TRUE (found version "5.1") -- 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 -- Checking for module 'htslib' -- Found htslib, version 1.22 -- Checking for module 'tabixpp' -- Package 'tabixpp' not found -- Using included tabixpp -- WFA using include /usr/local/include/wfa2lib -- Configuring done (20.3s) -- Generating done (0.5s) CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_SHARED_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED Python3_EXECUTABLE Python_EXECUTABLE -- Build files have been written to: /wrkdirs/usr/ports/biology/vcflib/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for vcflib-1.0.13 /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13 -B/wrkdirs/usr/ports/biology/vcflib/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/vcflib/work/.build//CMakeFiles/progress.marks /usr/local/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/bin/gmake -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' cd /wrkdirs/usr/ports/biology/vcflib/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/vcflib.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/bin/gmake -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 0%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman 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-I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -flto -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/fsom/fsom.c.o -MF CMakeFiles/vcflib.dir/contrib/fsom/fsom.c.o.d -o CMakeFiles/vcflib.dir/contrib/fsom/fsom.c.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fsom/fsom.c /usr/local/libexec/ccache/cc -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -flto -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o -MF CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o.d -o CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar/progress.c [ 13%] Building CXX object CMakeFiles/vcflib.dir/contrib/tabixpp/tabix.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIC -fopenmp=libomp -MD -MT CMakeFiles/vcflib.dir/contrib/tabixpp/tabix.cpp.o -MF CMakeFiles/vcflib.dir/contrib/tabixpp/tabix.cpp.o.d -o CMakeFiles/vcflib.dir/contrib/tabixpp/tabix.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp/tabix.cpp /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar/progress.c:79:49: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] 79 | fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds); | ~~~~ ^~~~~ | %lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar/progress.c:79:56: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] 79 | fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds); | ~~~~ ^~~~~~~ | %lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar/progress.c:79:65: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] 79 | fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds); | ~~~~ ^~~~~~~ | %lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar/progress.c:82:49: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] 82 | fprintf(stderr,"%llum %02llus ", minutes, seconds); | ~~~~ ^~~~~~~ | %lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar/progress.c:82:58: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] 82 | fprintf(stderr,"%llum %02llus ", minutes, seconds); | ~~~~~~ ^~~~~~~ | %02lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar/progress.c:85:49: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] 85 | fprintf(stderr,"%llu.%llus ", seconds, mseconds); | ~~~~ ^~~~~~~ | %lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar/progress.c:85:58: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] 85 | fprintf(stderr,"%llu.%llus ", seconds, mseconds); | ~~~~ ^~~~~~~~ | %lu 7 warnings generated. /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fsom/fsom.c:594:12: warning: taking the absolute value of unsigned type 'size_t' (aka 'unsigned long') has no effect [-Wabsolute-value] 594 | dist_i = abs( x - i ); | ^ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fsom/fsom.c:594:12: note: remove the call to 'abs' since unsigned values cannot be negative 594 | dist_i = abs( x - i ); | ^~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fsom/fsom.c:597:29: warning: taking the absolute value of unsigned type 'size_t' (aka 'unsigned long') has no effect [-Wabsolute-value] 597 | dist = pow( dist_i + abs ( y - j ), 4 ); | ^ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fsom/fsom.c:597:29: note: remove the call to 'abs' since unsigned values cannot be negative 597 | dist = pow( dist_i + abs ( y - j ), 4 ); | ^~~ 2 warnings generated. [ 13%] Linking CXX static library libvcflib.a /usr/local/bin/cmake -P CMakeFiles/vcflib.dir/cmake_clean_target.cmake /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcflib.dir/link.txt --verbose=1 "/usr/bin/llvm-ar" qc libvcflib.a CMakeFiles/vcflib.dir/src/legacy.cpp.o "CMakeFiles/vcflib.dir/src/vcf-wfa.cpp.o" "CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o" CMakeFiles/vcflib.dir/src/Variant.cpp.o CMakeFiles/vcflib.dir/src/rnglib.cpp.o CMakeFiles/vcflib.dir/src/var.cpp.o CMakeFiles/vcflib.dir/src/pdflib.cpp.o CMakeFiles/vcflib.dir/src/cdflib.cpp.o CMakeFiles/vcflib.dir/src/split.cpp.o CMakeFiles/vcflib.dir/src/stats.cpp.o CMakeFiles/vcflib.dir/src/index.cpp.o CMakeFiles/vcflib.dir/src/phase.cpp.o CMakeFiles/vcflib.dir/src/rkmh.cpp.o CMakeFiles/vcflib.dir/src/murmur3.cpp.o CMakeFiles/vcflib.dir/src/LeftAlign.cpp.o CMakeFiles/vcflib.dir/src/cigar.cpp.o CMakeFiles/vcflib.dir/src/allele.cpp.o CMakeFiles/vcflib.dir/contrib/fastahack/Fasta.cpp.o 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CMakeFiles/vcfstreamsort.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 29%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o [ 30%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o [ 31%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o [ 31%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o [ 30%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o [ 32%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman 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-I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -MF CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o.d -o 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-MD -MT CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -MF CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o.d -o CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcfcommonsamples.cpp [ 37%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o [ 37%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' cd /wrkdirs/usr/ports/biology/vcflib/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/vcfuniq.dir/DependInfo.cmake /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" 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/usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/smoother.dir/src/smoother.cpp.o -MF CMakeFiles/smoother.dir/src/smoother.cpp.o.d -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/smoother.cpp gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' cd /wrkdirs/usr/ports/biology/vcflib/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake [ 38%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" 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/usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/wcFst.dir/src/wcFst.cpp.o -MF CMakeFiles/wcFst.dir/src/wcFst.cpp.o.d -o CMakeFiles/wcFst.dir/src/wcFst.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/wcFst.cpp [ 39%] Building CXX object CMakeFiles/bFst.dir/src/bFst.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong 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-DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/bFst.dir/src/bFst.cpp.o -MF CMakeFiles/bFst.dir/src/bFst.cpp.o.d -o CMakeFiles/bFst.dir/src/bFst.cpp.o -c 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-std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -MF CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o.d -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcfprimers.cpp /usr/local/bin/gmake -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar 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/usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -MF CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o.d -o CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcfsitesummarize.cpp /usr/local/bin/gmake -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 41%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o [ 41%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o [ 42%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o [ 42%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include 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/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcfallelicprimitives.cpp /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/smoother.dir/link.d CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libhts.so /usr/lib/libomp.so [ 78%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack 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CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/vcfaltcount.dir/link.d CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libhts.so /usr/lib/libomp.so gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 78%] Built target vcfcommonsamples [ 78%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 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-pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -MF CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o.d -o CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcfinfosummarize.cpp /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/vcfprimers.dir/link.d CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libhts.so /usr/lib/libomp.so [ 79%] Built target vcfaddinfo gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 79%] Built target vcfafpath [ 80%] Built target smoother /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/vcfglxgt.dir/link.d CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libhts.so /usr/lib/libomp.so [ 80%] Built target vcfsitesummarize gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 80%] Built target vcfclassify /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcfld.cpp:246:16: warning: equality comparison result unused [-Wunused-comparison] 246 | derived == 1; | ~~~~~~~~^~~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcfld.cpp:246:16: note: use '=' to turn this equality comparison into an assignment 246 | derived == 1; | ^~ | = 1 warning generated. [ 80%] Built target vcfaltcount [ 80%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o [ 80%] Built target vcfnullgenofields [ 80%] Built target vcfprimers /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/vcfsamplediff.dir/link.d CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libhts.so /usr/lib/libomp.so [ 81%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcf-wfa.cpp [ 82%] Linking CXX executable vcfld gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 /usr/local/bin/gmake -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/legacy.cpp [ 82%] Built target vcfsamplediff [ 82%] Built target vcfglxgt /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/vcfrandom.dir/link.d CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libhts.so /usr/lib/libomp.so gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' cd /wrkdirs/usr/ports/biology/vcflib/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/vcfparsealts.dir/DependInfo.cmake /usr/local/bin/gmake -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' cd /wrkdirs/usr/ports/biology/vcflib/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" 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/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/sequenceDiversity.cpp:273:16: warning: equality comparison result unused [-Wunused-comparison] 273 | derived == 1; | ~~~~~~~~^~~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/sequenceDiversity.cpp:273:16: note: use '=' to turn this equality comparison into an assignment 273 | derived == 1; | ^~ | = 1 warning generated. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 82%] Built target vcfdistance /usr/local/bin/gmake -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build [ 82%] Linking CXX executable sequenceDiversity [ 82%] Built target vcfrandom /usr/local/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 /usr/local/bin/gmake -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/bin/gmake -f CMakeFiles/vcfwave.dir/build.make 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gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfroc.dir/src/legacy.cpp.o -MF CMakeFiles/vcfroc.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfroc.dir/src/legacy.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/legacy.cpp /usr/local/bin/gmake -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/build /usr/local/bin/gmake -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree 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CXX object CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o [ 84%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcf-wfa.cpp gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 84%] Built target vcfrandomsample [ 84%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar 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-DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -MF CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o.d -o 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-DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcf-wfa.cpp [ 86%] Building CXX object CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfwave.dir/src/legacy.cpp.o -MF CMakeFiles/vcfwave.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfwave.dir/src/legacy.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/legacy.cpp gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman 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'/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 86%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcfparsealts.cpp gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 86%] Built target vcfkeepinfo [ 86%] Building CXX object CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -Dpyvcflib_EXPORTS -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -isystem /usr/local/include/python3.11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIC -fvisibility=hidden -fopenmp=libomp -MD -MT CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -MF CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o.d -o CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/pythonffi.cpp [ 87%] Building CXX object CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include 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/usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/vcfevenregions.dir/link.d CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libhts.so /usr/lib/libomp.so gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 87%] Built target vcfevenregions [ 87%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem 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-fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcf-wfa.cpp [ 87%] Built target vcfcheck [ 87%] Built target vcffixup /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/vcfuniq.dir/link.d CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libhts.so /usr/lib/libomp.so gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/bFst.dir/link.d CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libhts.so /usr/lib/libomp.so [ 87%] Building CXX object CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o [ 87%] Built target vcfuniq /usr/local/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.13\" -DVERSION=\"1.0.13\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/contrib/tabixpp -I/usr/local/include/wfa2lib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcf-wfa.cpp gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include 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/wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfsample2info.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfdistance.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/abba-baba.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcf2tsv.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfbreakmulti.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfcreatemulti.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfsamplediff.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfstreamsort.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfaddinfo.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfentropy.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcflib.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfuniqalleles.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/sequenceDiversity.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfannotate.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfnullgenofields.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/normalize-iHS.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfevenregions.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/iHS.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfglxgt.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfintersect.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcffilter.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfgenosummarize.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfcommonsamples.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfleftalign.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfannotategenotypes.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/permuteGPAT++.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcf2dag.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfsitesummarize.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/smoother.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfcleancomplex.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/hapLrt.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/pyvcflib.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfallelicprimitives.1 -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/share/man/man1/vcfglbound.1 /bin/mv /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/libvcflib.a /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/lib ====> 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=2026-03-11T00:34:01+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=2b60f0ede764' '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 vcflib-1.0.13 ===> Building vcflib-1.0.13 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for vcflib-1.0.13 build of biology/vcflib | vcflib-1.0.13 ended at Tue Mar 10 20:35:48 EDT 2026 build time: 00:01:49