=>> Building biology/vcflib build started at Fri May 2 02:49:28 BST 2025 port directory: /usr/ports/biology/vcflib package name: vcflib-1.0.13 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1996 Apr 30 08:35 /usr/ports/biology/vcflib/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 39b2e62d29 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for 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=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- 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_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.2 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/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcflib-1.0.13 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> 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 => ekg-vcflib-v1.0.13_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.13?dummy=/ekg-vcflib-v1.0.13_GH0.tar.gz fetch: https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.13?dummy=/ekg-vcflib-v1.0.13_GH0.tar.gz: size unknown fetch: https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.13?dummy=/ekg-vcflib-v1.0.13_GH0.tar.gz: size of remote file is not known ekg-vcflib-v1.0.13_GH0.tar.gz 22 MB 6179 kBps 03s ===> 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/pybind11-2.13.6.pkg [pkg-builder.dan.net.uk] Installing pybind11-2.13.6... [pkg-builder.dan.net.uk] Extracting pybind11-2.13.6: .......... 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-builder.dan.net.uk] Installing py311-pypandoc-1.14_1... [pkg-builder.dan.net.uk] `-- Installing hs-pandoc-3.6.4... [pkg-builder.dan.net.uk] | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] `-- Extracting hs-pandoc-3.6.4: .......... done [pkg-builder.dan.net.uk] `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] Extracting py311-pypandoc-1.14_1: .......... done ===== Message from python311-3.11.12: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> 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-3.31.6.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.31.6... [pkg-builder.dan.net.uk] `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.6_1... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.51.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.51.0: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.31.6: .......... 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-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] 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-2.3.0_1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.3.0_1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.3.0_1,1: .......... done ===> 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-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> 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-1.21.pkg [pkg-builder.dan.net.uk] Installing htslib-1.21... [pkg-builder.dan.net.uk] `-- Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.21: .......... done ===> 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-builder.dan.net.uk] Installing wfa2-lib-2.3.5... [pkg-builder.dan.net.uk] 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 18.1.6 -- The CXX compiler identification is Clang 18.1.6 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/local/bin/pkgconf (found version "2.3.0") 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:50 (find_package) /usr/local/share/cmake/pybind11/pybind11Common.cmake:228 (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/python3.11 (found suitable version "3.11.12", minimum required is "3.7") -- Found PythonLibs: /usr/local/lib/libpython3.11.so -- Performing Test HAS_FLTO_THIN -- Performing Test HAS_FLTO_THIN - Success -- Found pybind11: /usr/local/include (found version "2.13.6") -- 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 "5.4.5") -- Found ZLIB: /usr/lib/libz.so (found version "1.3.1") -- Found CURL: /usr/local/lib/libcurl.so (found version "8.13.0") -- -- 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 1.21 -- Checking for module 'tabixpp' -- Package 'tabixpp' not found -- Using included tabixpp -- WFA using include /usr/local/include/wfa2lib -- Configuring done (3.4s) -- 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-1.0.13 /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/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=thin -fPIC -fopenmp=libomp -MD -MT CMakeFiles/vcflib.dir/src/rnglib.cpp.o -MF CMakeFiles/vcflib.dir/src/rnglib.cpp.o.d -o CMakeFiles/vcflib.dir/src/rnglib.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/rnglib.cpp [ 3%] Building CXX object CMakeFiles/vcflib.dir/src/var.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=thin -fPIC -fopenmp=libomp -MD -MT CMakeFiles/vcflib.dir/src/var.cpp.o -MF CMakeFiles/vcflib.dir/src/var.cpp.o.d -o CMakeFiles/vcflib.dir/src/var.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/var.cpp [ 3%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o /usr/local/libexec/ccache/c++ 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CMakeFiles/vcflib.dir/contrib/smithwaterman/Repeats.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=thin -fPIC -fopenmp=libomp -MD -MT 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-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=thin -fPIC -fopenmp=libomp -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-1.0.13/contrib/smithwaterman/disorder.cpp [ 11%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/LeftAlign.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=thin -fPIC -fopenmp=libomp -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-1.0.13/contrib/smithwaterman/LeftAlign.cpp [ 11%] Building C object CMakeFiles/vcflib.dir/contrib/fsom/fsom.c.o /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=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-1.0.13/contrib/fsom/fsom.c /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. [ 12%] Building C object CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o /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=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-1.0.13/contrib/filevercmp/filevercmp.c [ 12%] Building C object CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o /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=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-1.0.13/contrib/c-progress-bar/progress.c /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. [ 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=thin -fPIC 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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-1.0.13 /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/vcfallelicprimitives.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/bin/gmake -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 88%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.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=thin -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -MF 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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-1.0.13 /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/vcfcleancomplex.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/bin/gmake -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 89%] 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 -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=thin -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o.d -o 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-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=thin -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 [ 91%] Linking CXX executable vcfcleancomplex /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 /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=thin -fstack-protector-strong -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/vcfcleancomplex.dir/link.d CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o "CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o" -o vcfcleancomplex /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread /usr/local/lib/libwfa2.so.0 /usr/local/lib/libhts.so /usr/lib/libomp.so gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 91%] Built target vcfcleancomplex /usr/local/bin/gmake -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.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 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/usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++17 -flto=thin -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 [ 93%] Linking CXX executable vcfparsealts /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 /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=thin -fstack-protector-strong -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/vcfparsealts.dir/link.d CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o "CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o" -o vcfparsealts /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread libvcflib.a /usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/liblzma.so /usr/lib/libbz2.so -lpthread /usr/local/lib/libwfa2.so.0 /usr/local/lib/libhts.so /usr/lib/libomp.so gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 93%] Built target vcfparsealts /usr/local/bin/gmake -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.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/vcfroc.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/bin/gmake -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 94%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.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 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CMakeFiles/vcfstats.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/vcfstats.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/bin/gmake -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 95%] 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 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96%] Building CXX object CMakeFiles/vcfstats.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=thin -fPIE -fopenmp=libomp 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-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=thin -fPIE -fopenmp=libomp -MD -MT CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.13/src/vcf-wfa.cpp [ 97%] Linking CXX executable vcfstats /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 /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=thin -fstack-protector-strong -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/vcfstats.dir/link.d CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o 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/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=2025-05-02T01:49:28+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=39b2e62d29' '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 Fri May 2 02:59:19 BST 2025 build time: 00:09:52