=>> Building biology/vcflib build started at Sat Mar 30 23:51:19 GMT 2024 port directory: /usr/ports/biology/vcflib package name: vcflib-1.0.7_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1823 Mar 7 22:02 /usr/ports/biology/vcflib/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 44f5f66eff Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for vcflib-1.0.7_1: 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=gmake PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.9" 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=/ccache/libexec/ccache:/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" CCACHE_DIR="/root/.ccache" --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=/ccache/libexec/ccache:/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=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- ZIG="@comment " NO_ZIG="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 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/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcflib-1.0.7_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> vcflib-1.0.7_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcflib-1.0.7_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vcflib-1.0.7_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vcflib-1.0.7_1 for building => SHA256 Checksum OK for ekg-vcflib-v1.0.7_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-v1.1.2_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-1.0.7_1 for building ===> Extracting for vcflib-1.0.7_1 => SHA256 Checksum OK for ekg-vcflib-v1.0.7_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-v1.1.2_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-1.0.7_1 ===> Applying FreeBSD patches for vcflib-1.0.7_1 from /usr/ports/biology/vcflib/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcflib-1.0.7_1 depends on package: pybind11>0 - not found ===> Installing existing package /packages/All/pybind11-2.11.1.pkg [pkg-builder.dan.net.uk] Installing pybind11-2.11.1... [pkg-builder.dan.net.uk] Extracting pybind11-2.11.1: .......... done ===> vcflib-1.0.7_1 depends on package: pybind11>0 - found ===> Returning to build of vcflib-1.0.7_1 ===> vcflib-1.0.7_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.28.3... [pkg-builder.dan.net.uk] `-- Installing expat-2.6.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.5... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.5: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.48.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.48.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.28.3: .......... done ===> vcflib-1.0.7_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of vcflib-1.0.7_1 ===> vcflib-1.0.7_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> vcflib-1.0.7_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of vcflib-1.0.7_1 ===> vcflib-1.0.7_1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.1.1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.1.1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.1.1,1: .......... done ===> vcflib-1.0.7_1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of vcflib-1.0.7_1 ===> vcflib-1.0.7_1 depends on file: /usr/local/bin/python3.9 - not found ===> Installing existing package /packages/All/python39-3.9.18_1.pkg [pkg-builder.dan.net.uk] Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] Extracting python39-3.9.18_1: .......... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> vcflib-1.0.7_1 depends on file: /usr/local/bin/python3.9 - found ===> Returning to build of vcflib-1.0.7_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcflib-1.0.7_1 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.17_1.pkg [pkg-builder.dan.net.uk] Installing htslib-1.17_1... [pkg-builder.dan.net.uk] `-- Installing curl-8.6.0... [pkg-builder.dan.net.uk] | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libidn2-2.3.7... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.2... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.7: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.60.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.60.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing librtmp-2.4.20190330_1... [pkg-builder.dan.net.uk] | `-- Extracting librtmp-2.4.20190330_1: ......... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.0_1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.0_1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.6.0: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.19... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.19: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.17_1: .......... done ===> vcflib-1.0.7_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of vcflib-1.0.7_1 ===> vcflib-1.0.7_1 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> vcflib-1.0.7_1 depends on shared library: libwfa2.so - not found ===> Installing existing package /packages/All/wfa2-lib-2.3.4.pkg [pkg-builder.dan.net.uk] Installing wfa2-lib-2.3.4... [pkg-builder.dan.net.uk] Extracting wfa2-lib-2.3.4: .......... done ===> vcflib-1.0.7_1 depends on shared library: libwfa2.so - found (/usr/local/lib/libwfa2.so) ===> Returning to build of vcflib-1.0.7_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for vcflib-1.0.7_1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/vcflib/work/.build -- The C compiler identification is Clang 14.0.5 -- The CXX compiler identification is Clang 14.0.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /ccache/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /ccache/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/local/bin/pkgconf (found version "2.1.1") CMake Warning (dev) at /usr/local/share/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package): 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. Call Stack (most recent call first): /usr/local/share/cmake/pybind11/pybind11Tools.cmake:50 (find_package) /usr/local/share/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/local/share/cmake/pybind11/pybind11Config.cmake:250 (include) CMakeLists.txt:19 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/local/bin/python3.9 (found suitable version "3.9.18", minimum required is "3.6") -- Found PythonLibs: /usr/local/lib/libpython3.9.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Performing Test HAS_FLTO_THIN -- Performing Test HAS_FLTO_THIN - Success -- Found pybind11: /usr/local/include (found version "2.11.1") -- 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 "5.4.1") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.13") -- Found CURL: /usr/local/lib/libcurl.so (found version "8.6.0") -- -- Found OpenMP_C: -fopenmp=libomp (found version "5.0") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0") -- Found OpenMP: TRUE (found version "5.0") -- 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 1.17 -- Checking for module 'tabixpp' -- Package 'tabixpp', required by 'virtual:world', not found -- WFA using include /usr/local/include/wfa2lib Pandoc needs to be installed to generate the man pages -- Configuring done (6.3s) -- Generating done (0.7s) 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-1.0.7_1 /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 -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 gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' 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-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 /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' 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/vcf-c-api.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree 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-flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/Variant.cpp.o -MF CMakeFiles/vcflib.dir/src/Variant.cpp.o.d -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/Variant.cpp /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/Variant.cpp:1112:30: warning: decomposition declarations are a C++17 extension [-Wc++17-extensions] for (const auto& [name1, value]: var.info) ^~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/Variant.cpp:1114:30: warning: decomposition declarations are a C++17 extension [-Wc++17-extensions] for (const auto& [name2, value]: var.infoFlags) ^~~~~~~~~~~~~~ 2 warnings generated. [ 2%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/rnglib.cpp.o -MF 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-I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/pdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/pdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/pdflib.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/pdflib.cpp [ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman 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-DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/rkmh.cpp.o -MF CMakeFiles/vcflib.dir/src/rkmh.cpp.o.d -o CMakeFiles/vcflib.dir/src/rkmh.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/rkmh.cpp [ 5%] Building CXX object CMakeFiles/vcflib.dir/src/murmur3.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 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-I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/cigar.cpp.o -MF CMakeFiles/vcflib.dir/src/cigar.cpp.o.d -o CMakeFiles/vcflib.dir/src/cigar.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/cigar.cpp [ 6%] Building CXX object CMakeFiles/vcflib.dir/src/allele.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/allele.cpp.o -MF CMakeFiles/vcflib.dir/src/allele.cpp.o.d -o CMakeFiles/vcflib.dir/src/allele.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/allele.cpp [ 7%] Building CXX object CMakeFiles/vcflib.dir/contrib/fastahack/Fasta.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/fastahack/Fasta.cpp.o -MF CMakeFiles/vcflib.dir/contrib/fastahack/Fasta.cpp.o.d -o CMakeFiles/vcflib.dir/contrib/fastahack/Fasta.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack/Fasta.cpp [ 7%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/SmithWatermanGotoh.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/smithwaterman/SmithWatermanGotoh.cpp.o -MF CMakeFiles/vcflib.dir/contrib/smithwaterman/SmithWatermanGotoh.cpp.o.d -o CMakeFiles/vcflib.dir/contrib/smithwaterman/SmithWatermanGotoh.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman/SmithWatermanGotoh.cpp [ 8%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/Repeats.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/smithwaterman/Repeats.cpp.o -MF CMakeFiles/vcflib.dir/contrib/smithwaterman/Repeats.cpp.o.d -o CMakeFiles/vcflib.dir/contrib/smithwaterman/Repeats.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman/Repeats.cpp [ 8%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/IndelAllele.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/smithwaterman/IndelAllele.cpp.o -MF CMakeFiles/vcflib.dir/contrib/smithwaterman/IndelAllele.cpp.o.d -o CMakeFiles/vcflib.dir/contrib/smithwaterman/IndelAllele.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman/IndelAllele.cpp [ 9%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/disorder.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/smithwaterman/disorder.cpp.o -MF CMakeFiles/vcflib.dir/contrib/smithwaterman/disorder.cpp.o.d -o CMakeFiles/vcflib.dir/contrib/smithwaterman/disorder.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman/disorder.cpp [ 10%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/LeftAlign.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/smithwaterman/LeftAlign.cpp.o -MF CMakeFiles/vcflib.dir/contrib/smithwaterman/LeftAlign.cpp.o.d -o CMakeFiles/vcflib.dir/contrib/smithwaterman/LeftAlign.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman/LeftAlign.cpp [ 10%] Building C object CMakeFiles/vcflib.dir/contrib/fsom/fsom.c.o /ccache/libexec/ccache/cc -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -flto=thin -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-1.0.7/contrib/fsom/fsom.c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fsom/fsom.c:594:12: warning: taking the absolute value of unsigned type 'unsigned long' has no effect [-Wabsolute-value] dist_i = abs( x - i ); ^ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fsom/fsom.c:594:12: note: remove the call to 'abs' since unsigned values cannot be negative dist_i = abs( x - i ); ^~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fsom/fsom.c:597:29: warning: taking the absolute value of unsigned type 'unsigned long' has no effect [-Wabsolute-value] dist = pow( dist_i + abs ( y - j ), 4 ); ^ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fsom/fsom.c:597:29: note: remove the call to 'abs' since unsigned values cannot be negative dist = pow( dist_i + abs ( y - j ), 4 ); ^~~~ 2 warnings generated. [ 11%] Building C object CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o /ccache/libexec/ccache/cc -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o -MF CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o.d -o CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp/filevercmp.c [ 11%] Building C object CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o /ccache/libexec/ccache/cc -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -flto=thin -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-1.0.7/contrib/c-progress-bar/progress.c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/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] fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds); ~~~~ ^~~~~ %lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/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] fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds); ~~~~ ^~~~~~~ %lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/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] fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds); ~~~~ ^~~~~~~ %lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/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] fprintf(stderr,"%llum %02llus ", minutes, seconds); ~~~~ ^~~~~~~ %lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/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] fprintf(stderr,"%llum %02llus ", minutes, seconds); ~~~~~~ ^~~~~~~ %02lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/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] fprintf(stderr,"%llu.%llus ", seconds, mseconds); ~~~~ ^~~~~~~ %lu /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/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] fprintf(stderr,"%llu.%llus ", seconds, mseconds); ~~~~ ^~~~~~~~ %lu 7 warnings generated. [ 12%] Building CXX object CMakeFiles/vcflib.dir/contrib/tabixpp/tabix.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -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-1.0.7/contrib/tabixpp/tabix.cpp [ 12%] 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" cr libvcflib.a "CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o" CMakeFiles/vcflib.dir/src/legacy.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/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 CMakeFiles/vcflib.dir/contrib/smithwaterman/SmithWatermanGotoh.cpp.o CMakeFiles/vcflib.dir/contrib/smithwaterman/Repeats.cpp.o CMakeFiles/vcflib.dir/contrib/smithwaterman/IndelAllele.cpp.o CMakeFiles/vcflib.dir/contrib/smithwaterman/disorder.cpp.o CMakeFiles/vcflib.dir/contrib/smithwaterman/LeftAlign.cpp.o CMakeFiles/vcflib.dir/contrib/fsom/fsom.c.o CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o "CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o" CMakeFiles/vcflib.dir/contrib/tabixpp/tabix.cpp.o "/usr/bin/llvm-ranlib" libvcflib.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 12%] Built target vcflib gmake -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.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" 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/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/pFst.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 25%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman 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/usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread /usr/local/lib/libhts.so libvcflib.a /usr/local/lib/libwfa2.so gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 58%] Built target vcfnumalt gmake -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.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-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build gmake[2]: Entering directory 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-fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto=thin -fstack-protector-strong -L/usr/local/lib CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate -lhts /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread /usr/local/lib/libhts.so libvcflib.a /usr/local/lib/libwfa2.so gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 61%] Built target vcfannotate gmake -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.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-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/.build 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-I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIE -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfallelicprimitives.cpp [ 62%] Linking CXX executable vcfallelicprimitives /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 /ccache/libexec/ccache/c++ -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto=thin -fstack-protector-strong -L/usr/local/lib CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -lhts /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread /usr/local/lib/libhts.so libvcflib.a /usr/local/lib/libwfa2.so gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 62%] Built target vcfallelicprimitives gmake -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.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-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/vcfwave.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 63%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o /ccache/libexec/ccache/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIE -MD -MT CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o -MF CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o.d -o CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfwave.cpp /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfwave.cpp:290:29: warning: decomposition declarations are a C++17 extension [-Wc++17-extensions] for (const auto [alt0, wfvalue] : varAlleles) { ^~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfwave.cpp:341:23: warning: decomposition declarations are a C++17 extension [-Wc++17-extensions] for (auto [tag,aln]: unique) { ^~~~~~~~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfwave.cpp:361:23: warning: decomposition declarations are a C++17 extension [-Wc++17-extensions] for (auto [key,v] : unique) { ^~~~~~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfwave.cpp:392:23: warning: decomposition declarations are a C++17 extension [-Wc++17-extensions] for (auto [key,v] : track_variants) { ^~~~~~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfwave.cpp:419:23: warning: decomposition declarations are a C++17 extension [-Wc++17-extensions] for (auto [key,v]: track_variants) { ^~~~~~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfwave.cpp:429:31: warning: decomposition declarations are a C++17 extension [-Wc++17-extensions] for (auto [key2,var2]: track_variants) { ^~~~~~~~~~~ /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfwave.cpp:461:23: warning: decomposition declarations are a C++17 extension [-Wc++17-extensions] for (auto [key,v]: track_variants) { ^~~~~~~ 7 warnings generated. [ 63%] Linking CXX executable vcfwave /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcfwave.dir/link.txt --verbose=1 /ccache/libexec/ccache/c++ -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto=thin -fstack-protector-strong -L/usr/local/lib CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o -o vcfwave -lhts /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread /usr/local/lib/libhts.so libvcflib.a /usr/local/lib/libwfa2.so gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 63%] Built target vcfwave gmake -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.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-1.0.7 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/usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIE -MD -MT CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -MF CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o.d -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfaddinfo.cpp [ 65%] Linking CXX executable vcfaddinfo /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 /ccache/libexec/ccache/c++ -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto=thin -fstack-protector-strong -L/usr/local/lib CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -o vcfaddinfo -lhts /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread /usr/local/lib/libhts.so libvcflib.a /usr/local/lib/libwfa2.so gmake[2]: Leaving directory 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-I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIE -MD -MT CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -MF CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o.d -o CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfkeepgeno.cpp [ 67%] Linking CXX executable vcfkeepgeno /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 /ccache/libexec/ccache/c++ 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-I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIE -MD -MT CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -MF CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o.d -o CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfafpath.cpp [ 68%] Linking CXX executable vcfafpath /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1 /ccache/libexec/ccache/c++ -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto=thin -fstack-protector-strong -L/usr/local/lib 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/usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIE -MD -MT CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -MF CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o.d -o CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcfremap.cpp [ 80%] Linking CXX executable vcfremap /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1 /ccache/libexec/ccache/c++ -fopenmp=libomp -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto=thin -fstack-protector-strong -L/usr/local/lib CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -lhts /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread /usr/local/lib/libhts.so libvcflib.a /usr/local/lib/libwfa2.so gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 80%] Built 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/wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake[2]: Nothing to be done for 'CMakeFiles/vcfgenotypes.dir/build'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 41%] Built target vcfgenotypes gmake -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.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-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 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cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/vcfecho -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/dumpContigsFromHeader -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/bFst -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/pVst -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/hapLrt -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/popStats -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/wcFst -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/iHS -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/segmentFst -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/segmentIhs -- Installing: /wrkdirs/usr/ports/biology/vcflib/work/stage/usr/local/bin/genotypeSummary -- Installing: 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/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=2024-03-30T23:51:19+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=44f5f66eff' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for vcflib-1.0.7_1 ===> Building vcflib-1.0.7_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for vcflib-1.0.7_1 build of biology/vcflib | vcflib-1.0.7_1 ended at Sun Mar 31 00:13:00 GMT 2024 build time: 00:21:42