=>> Building biology/btllib build started at Sun Sep 28 09:55:22 EDT 2025 port directory: /usr/ports/biology/btllib package name: btllib-1.7.5 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 970 Dec 8 2024 /usr/ports/biology/btllib/Makefile Ports top last git commit: a936fb9b16ba Ports top unclean checkout: no Port dir last git commit: bec50be298b0 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500064 Jail OSVERSION: 1500064 Job Id: 15 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/15/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix /usr/local --localstatedir /var --infodir share/info --auto-features=enabled -Dpython.bytecompile=-1 -Db_colorout=never --buildtype release --optimization plain --strip _build --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/btllib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/btllib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/btllib/work/.cache HOME=/wrkdirs/usr/ports/biology/btllib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/btllib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/btllib/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/btllib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/btllib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/btllib/work/.cache HOME=/wrkdirs/usr/ports/biology/btllib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/btllib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/btllib/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 DESTDIR=/wrkdirs/usr/ports/biology/btllib/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/btllib" EXAMPLESDIR="share/examples/btllib" DATADIR="share/btllib" WWWDIR="www/btllib" ETCDIR="etc/btllib" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/btllib DOCSDIR=/usr/local/share/doc/btllib EXAMPLESDIR=/usr/local/share/examples/btllib WWWDIR=/usr/local/www/btllib ETCDIR=/usr/local/etc/btllib --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> btllib-1.7.5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1.pkg [pkg.DaveG.ca] Installing pkg-2.3.1... [pkg.DaveG.ca] Extracting pkg-2.3.1: .......... done ===> btllib-1.7.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of btllib-1.7.5 =========================================================================== =================================================== ===== 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 btllib-1.7.5 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by btllib-1.7.5 for building => SHA256 Checksum OK for bcgsc-btllib-v1.7.5_GH0.tar.gz. => SHA256 Checksum OK for p-ranav-argparse-15d745f_GH0.tar.gz. => SHA256 Checksum OK for skystrife-cpptoml-fededad_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 btllib-1.7.5 for building ===> Extracting for btllib-1.7.5 => SHA256 Checksum OK for bcgsc-btllib-v1.7.5_GH0.tar.gz. => SHA256 Checksum OK for p-ranav-argparse-15d745f_GH0.tar.gz. => SHA256 Checksum OK for skystrife-cpptoml-fededad_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 btllib-1.7.5 ===> Applying FreeBSD patches for btllib-1.7.5 from /usr/ports/biology/btllib/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> btllib-1.7.5 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.3_1.pkg [pkg.DaveG.ca] Installing bash-5.3.3_1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] Extracting bash-5.3.3_1: .......... done ===> btllib-1.7.5 depends on executable: bash - found ===> Returning to build of btllib-1.7.5 ===> btllib-1.7.5 depends on executable: samtools - not found ===> Installing existing package /packages/All/samtools-1.22.pkg [pkg.DaveG.ca] Installing samtools-1.22... [pkg.DaveG.ca] `-- Installing htslib-1.22... [pkg.DaveG.ca] | `-- Installing curl-8.15.0... [pkg.DaveG.ca] | | `-- Installing brotli-1.1.0,1... [pkg.DaveG.ca] | | `-- Extracting brotli-1.1.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing libunistring-1.3... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.3: .......... done [pkg.DaveG.ca] | | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | | `-- Installing libnghttp2-1.67.0... [pkg.DaveG.ca] | | `-- Extracting libnghttp2-1.67.0: ....... done [pkg.DaveG.ca] | | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7... [pkg.DaveG.ca] | | `-- Installing liblz4-1.10.0,1... [pkg.DaveG.ca] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7: .......... done [pkg.DaveG.ca] | `-- Extracting curl-8.15.0: .......... done [pkg.DaveG.ca] | `-- Installing libdeflate-1.24... [pkg.DaveG.ca] | `-- Extracting libdeflate-1.24: .......... done [pkg.DaveG.ca] `-- Extracting htslib-1.22: .......... done [pkg.DaveG.ca] Extracting samtools-1.22: .......... done ===> btllib-1.7.5 depends on executable: samtools - found ===> Returning to build of btllib-1.7.5 ===> btllib-1.7.5 depends on executable: cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.7_1.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.7_1... [pkg.DaveG.ca] `-- Installing expat-2.7.2... [pkg.DaveG.ca] `-- Extracting expat-2.7.2: .......... done [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.51.0... [pkg.DaveG.ca] `-- Extracting libuv-1.51.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.4_1... [pkg.DaveG.ca] `-- Extracting rhash-1.4.4_1: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.7_1: .......... done ===> btllib-1.7.5 depends on executable: cmake - found ===> Returning to build of btllib-1.7.5 ===> btllib-1.7.5 depends on executable: meson - not found ===> Installing existing package /packages/All/meson-1.7.0.pkg [pkg.DaveG.ca] Installing meson-1.7.0... [pkg.DaveG.ca] `-- Installing ninja-1.13.1,4... [pkg.DaveG.ca] | `-- Installing python311-3.11.13_1... [pkg.DaveG.ca] | | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | | `-- Installing readline-8.2.13_2... [pkg.DaveG.ca] | | `-- Extracting readline-8.2.13_2: .......... done [pkg.DaveG.ca] | `-- Extracting python311-3.11.13_1: .......... done [pkg.DaveG.ca] `-- Extracting ninja-1.13.1,4: ..... done [pkg.DaveG.ca] Extracting meson-1.7.0: .......... done ===== Message from python311-3.11.13_1: -- 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 ===> btllib-1.7.5 depends on executable: meson - found ===> Returning to build of btllib-1.7.5 ===> btllib-1.7.5 depends on executable: ninja - found ===> btllib-1.7.5 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> btllib-1.7.5 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of btllib-1.7.5 ===> btllib-1.7.5 depends on file: /usr/local/bin/python3.11 - found ===> btllib-1.7.5 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> btllib-1.7.5 depends on file: /usr/local/bin/ccache - found ===> Returning to build of btllib-1.7.5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> btllib-1.7.5 depends on shared library: libsdsl.so - not found ===> Installing existing package /packages/All/sdsl-lite-2.1.1.137.pkg [pkg.DaveG.ca] Installing sdsl-lite-2.1.1.137... [pkg.DaveG.ca] Extracting sdsl-lite-2.1.1.137: .......... done ===> btllib-1.7.5 depends on shared library: libsdsl.so - found (/usr/local/lib/libsdsl.so) ===> Returning to build of btllib-1.7.5 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for btllib-1.7.5 WARNING: Recommend using either -Dbuildtype or -Doptimization + -Ddebug. Using both is redundant since they override each other. See: https://mesonbuild.com/Builtin-options.html#build-type-options The Meson build system Version: 1.7.0 Source dir: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5 Build dir: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build Build type: native build Project name: btllib Project version: 1.7.5 C++ compiler for the host machine: c++ (clang 19.1.7 "FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)") C++ linker for the host machine: c++ ld.lld 19.1.7 Host machine cpu family: x86_64 Host machine cpu: x86_64 Configuring config.hpp using configuration Run-time dependency threads found: YES Run-time dependency OpenMP found: YES 5.1 Executing subproject cpptoml method cmake cpptoml| Found CMake: /usr/local/bin/cmake (3.31.7) | Configuring the build directory with CMake version 3.31.7 | Running CMake with: -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release | - build directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/subprojects/cpptoml/__CMake_build | - source directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/subprojects/cpptoml | - toolchain file: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/subprojects/cpptoml/__CMake_build/CMakeMesonToolchainFile.cmake | - preload file: /usr/local/lib/python3.11/site-packages/mesonbuild/cmake/data/preload.cmake | - trace args: --trace-expand --trace-format=json-v1 --no-warn-unused-cli --trace-redirect=cmake_trace.txt | - disabled policy warnings: [CMP0025, CMP0047, CMP0056, CMP0060, CMP0065, CMP0066, CMP0067, CMP0082, CMP0089, CMP0102] | CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): | Compatibility with CMake < 3.10 will be removed from a future version of | CMake. | Update the VERSION argument value. Or, use the ... syntax | to tell CMake that the project requires at least but has been updated | to work with policies introduced by or earlier. | Put cmake in trace mode, but with variables expanded. | Put cmake in trace mode and sets the trace output format. | Not searching for unused variables given on the command line. | Put cmake in trace mode and redirect trace output to a file instead of stderr. | Trace will be written to cmake_trace.txt | -- The C compiler identification is Clang 19.1.7 | -- The CXX compiler identification is Clang 19.1.7 | CMake Warning (dev) at /usr/local/share/cmake/Modules/CMakeFindBinUtils.cmake:225 (find_program): | Policy CMP0126 is not set: set(CACHE) does not remove a normal variable of | the same name. Run "cmake --help-policy CMP0126" for policy details. Use | the cmake_policy command to set the policy and suppress this warning. | For compatibility with older versions of CMake, normal variable | "CMAKE_TAPI" will be removed from the current scope. | Call Stack (most recent call first): | /usr/local/share/cmake/Modules/CMakeDetermineCXXCompiler.cmake:207 (include) | CMakeLists.txt:2 (project) | This warning is for project developers. Use -Wno-dev to suppress it. | -- 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 | -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) | -- Configuring done (5.7s) | -- Generating done (0.1s) | -- Build files have been written to: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/subprojects/cpptoml/__CMake_build cpptoml| CMake configuration: SUCCEEDED cpptoml| CMake project cpptoml has 1 build targets. cpptoml| Generated Meson AST: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/subprojects/cpptoml/meson.build cpptoml| Project name: cpptoml cpptoml| Project version: undefined cpptoml| Build targets in project: 0 cpptoml| Subproject cpptoml finished. Found pkg-config: YES (/usr/local/bin/pkgconf) 2.4.3 Run-time dependency sdsl-lite found: YES 2.1.0 Executing subproject argparse method cmake | Configuring the build directory with CMake version 3.31.7 | Running CMake with: -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release | - build directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/subprojects/argparse/__CMake_build | - source directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/subprojects/argparse | - toolchain file: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/subprojects/argparse/__CMake_build/CMakeMesonToolchainFile.cmake | - preload file: /usr/local/lib/python3.11/site-packages/mesonbuild/cmake/data/preload.cmake | - trace args: --trace-expand --trace-format=json-v1 --no-warn-unused-cli --trace-redirect=cmake_trace.txt | - disabled policy warnings: [CMP0025, CMP0047, CMP0056, CMP0060, CMP0065, CMP0066, CMP0067, CMP0082, CMP0089, CMP0102] | Put cmake in trace mode, but with variables expanded. | Put cmake in trace mode and sets the trace output format. | Not searching for unused variables given on the command line. | Put cmake in trace mode and redirect trace output to a file instead of stderr. | Trace will be written to cmake_trace.txt | -- The CXX compiler identification is Clang 19.1.7 | -- 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 | -- Configuring done (1.2s) | -- Generating done (0.1s) | -- Build files have been written to: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/subprojects/argparse/__CMake_build argparse| CMake configuration: SUCCEEDED argparse| CMake project argparse 2.9.0 has 1 build targets. argparse| Generated Meson AST: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/subprojects/argparse/meson.build argparse| Project name: argparse argparse| Project version: 2.9.0 argparse| Build targets in project: 0 argparse| Subproject argparse finished. Program samtools found: YES (/usr/local/bin/samtools) Program gzip found: YES (/usr/bin/gzip) Program xz found: YES (/usr/bin/xz) Program bzip2 found: YES (/usr/bin/bzip2) Program tar found: YES (/usr/bin/tar) Program gcovr found: NO Program swig found: NO Program doxygen found: NO WARNING: You should add the boolean check kwarg to the run_command call. It currently defaults to false, but it will default to true in meson 2.0. See also: https://github.com/mesonbuild/meson/issues/9300 Program python3 found: YES (/wrkdirs/usr/ports/biology/btllib/work/.bin/python3) Program python3-config found: NO Message: python3-config not found, skipping Python wrappers. Build targets in project: 11 btllib 1.7.5 Subprojects argparse : YES cpptoml : YES User defined options auto_features : enabled b_colorout : never buildtype : release infodir : share/info localstatedir : /var optimization : plain prefix : /usr/local python.bytecompile: -1 strip : true Found ninja-1.13.1 at /usr/local/bin/ninja WARNING: Need gcovr or lcov/genhtml to generate any coverage reports WARNING: Running the setup command as `meson [options]` instead of `meson setup [options]` is ambiguous and deprecated. =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for btllib-1.7.5 [ 4% 16/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never 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libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_bloom_filter.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_bloom_filter.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/bloom_filter.cpp [ 75% 20/24] c++ -o libbtllib.so libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_fasta_module.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_multiline_fasta_module.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_sam_module.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_aahash.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_data_stream.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_writer.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_randseq.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_process_pipeline.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_multiline_fastq_module.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_util.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_bloom_filter.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_fastq_module.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_status.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_cstring.cpp.o --coverage -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,-soname,libbtllib.so -Wl,--start-group -ldl -lstdc++ -lm -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -pthread -fopenmp /usr/local/lib/libsdsl.so /usr/local/lib/libdivsufsort.so /usr/local/lib/libdivsufsort64.so -Wl,--end-group [ 79% 21/24] c++ -Irecipes/randseq.p -Irecipes -I../recipes -Iinclude -I../include -I. -I.. -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I../subprojects/argparse/include -Isubprojects/argparse/__CMake_build -I../subprojects/argparse/__CMake_build -Isubprojects/argparse -I../subprojects/argparse -I/usr/local/include -fdiagnostics-color=never --coverage -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -pthread -MD -MQ recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_randseq.cpp.o -MF recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_randseq.cpp.o.d -o recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_randseq.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/recipes/randseq.cpp [ 83% 21/24] /usr/local/bin/meson --internal symbolextractor /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build libbtllib.so libbtllib.so libbtllib.so.p/libbtllib.so.symbols [ 87% 23/24] c++ -o recipes/indexlr recipes/indexlr.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_indexlr.cpp.o --coverage -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -ldl -lstdc++ -lm -O2 -pipe -fstack-protector-strong -fno-strict-aliasing '-Wl,-rpath,$ORIGIN/..:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/ -Wl,-rpath-link,/usr/local/lib libbtllib.so -pthread -fopenmp /usr/local/lib/libsdsl.so /usr/local/lib/libdivsufsort.so /usr/local/lib/libdivsufsort64.so -Wl,--end-group [ 91% 23/24] c++ -o recipes/randseq recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_randseq.cpp.o --coverage -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -ldl -lstdc++ -lm -O2 -pipe -fstack-protector-strong -fno-strict-aliasing '-Wl,-rpath,$ORIGIN/..:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/ -Wl,-rpath-link,/usr/local/lib libbtllib.so -pthread -fopenmp /usr/local/lib/libsdsl.so /usr/local/lib/libdivsufsort.so /usr/local/lib/libdivsufsort64.so -Wl,--end-group [ 95% 23/24] c++ -Irecipes/mi_bf_generate.p -Irecipes -I../recipes -Iinclude -I../include -I. -I.. -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -pthread -MD -MQ recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_mi_bloom_filter.cpp.o -MF recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_mi_bloom_filter.cpp.o.d -o recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_mi_bloom_filter.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/recipes/mi_bloom_filter.cpp In file included from /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/recipes/mi_bloom_filter.cpp:1: In file included from ../include/btllib/mi_bloom_filter.hpp:17: In file included from /usr/local/include/sdsl/bit_vector_il.hpp:25: In file included from /usr/local/include/sdsl/int_vector.hpp:26: /usr/local/include/sdsl/util.hpp:492:19: warning: variable 'vals' set but not used [-Wunused-but-set-variable] 492 | uint64_t n=0, vals=0; | ^ 1 warning generated. [100% 24/24] c++ -o recipes/mi_bf_generate recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_mi_bloom_filter.cpp.o --coverage -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -ldl -lstdc++ -lm -O2 -pipe -fstack-protector-strong -fno-strict-aliasing '-Wl,-rpath,$ORIGIN/..:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/ -Wl,-rpath-link,/usr/local/lib libbtllib.so -pthread -fopenmp /usr/local/lib/libsdsl.so /usr/local/lib/libdivsufsort.so /usr/local/lib/libdivsufsort64.so -Wl,--end-group =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> btllib-1.7.5 depends on executable: samtools - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for btllib-1.7.5 ===> Generating temporary packing list [ 0% 1/1] /usr/local/bin/meson install --no-rebuild Installing libbtllib.so to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/lib Stripping target 'libbtllib.so'. Installing recipes/indexlr to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/bin Stripping target 'recipes/indexlr'. Installing recipes/randseq to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/bin Stripping target 'recipes/randseq'. Installing recipes/mi_bf_generate to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/bin Stripping target 'recipes/mi_bf_generate'. Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/status.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/hashing_internals.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/graph.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/seq_reader_multiline_fasta_module.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/nthash_seed.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/order_queue.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/seq_reader_fastq_module.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/counting_bloom_filter-inl.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/mi_bloom_filter.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/mi_bloom_filter-inl.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/seq_reader.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/seq_reader_fasta_module.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/seq_writer.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/util.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/seq.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/data_stream.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/seq_reader_multiline_fastq_module.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/nthash_kmer.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/aahash.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/seq_reader_sam_module.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/process_pipeline.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/nthash.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/bloom_filter.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/counting_bloom_filter.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/cstring.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/randseq.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Installing /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/include/btllib/indexlr.hpp to /wrkdirs/usr/ports/biology/btllib/work/stage/usr/local/include/btllib Running custom install script '/wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/scripts/install-cpptoml' ====> 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=2025-09-28T13:55:22+0000' 'PKG_NOTE_ports_top_git_hash=a936fb9b16ba' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=bec50be298b0' '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 btllib-1.7.5 ===> Building btllib-1.7.5 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for btllib-1.7.5 build of biology/btllib | btllib-1.7.5 ended at Sun Sep 28 09:56:29 EDT 2025 build time: 00:01:10