=>> Building biology/btllib build started at Sat May 3 00:01:36 BST 2025 port directory: /usr/ports/biology/btllib package name: btllib-1.7.5 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 970 Dec 29 14:16 /usr/ports/biology/btllib/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 07 ---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/07/.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--- ---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=" -fstack-protector-strong " 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=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/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=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/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--- 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 ===> btllib-1.7.5 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 ===> 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-5.2.37.pkg [pkg-builder.dan.net.uk] Installing bash-5.2.37... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.23.1... [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 gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting bash-5.2.37: .......... 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-1.21.pkg [pkg-builder.dan.net.uk] Installing samtools-1.21... [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 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 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] | | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.16,1: .......... done [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 [pkg-builder.dan.net.uk] Extracting samtools-1.21: .......... 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-3.31.6.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 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 ===> 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-builder.dan.net.uk] Installing meson-1.7.0... [pkg-builder.dan.net.uk] `-- Installing ninja-1.11.1,4... [pkg-builder.dan.net.uk] | `-- Installing python311-3.11.12... [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] | | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | | `-- Extracting mpdecimal-4.0.0: .......... 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 ninja-1.11.1,4: ..... done [pkg-builder.dan.net.uk] Extracting meson-1.7.0: .......... 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 ===> 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-2.3.0_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 ===> 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-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. ===> 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-builder.dan.net.uk] Installing sdsl-lite-2.1.1.137... [pkg-builder.dan.net.uk] 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 18.1.6 "FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)") C++ linker for the host machine: c++ ld.lld 18.1.6 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 (3.31.6) | Configuring the build directory with CMake version 3.31.6 | 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 18.1.6 | -- The CXX compiler identification is Clang 18.1.6 | 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 (3.0s) | -- 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) 2.3.0 Run-time dependency sdsl-lite found: YES 2.1.0 Executing subproject argparse method cmake | Configuring the build directory with CMake version 3.31.6 | 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 18.1.6 | -- 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 (1.8s) | -- 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-1.11.1 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% 1/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_fasta_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_fasta_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_fasta_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/seq_reader_fasta_module.cpp [ 8% 2/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_multiline_fasta_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_multiline_fasta_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_multiline_fasta_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/seq_reader_multiline_fasta_module.cpp [ 12% 3/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/seq.cpp [ 16% 4/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_sam_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_sam_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_sam_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/seq_reader_sam_module.cpp [ 20% 5/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/seq_reader.cpp [ 25% 6/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_aahash.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_aahash.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_aahash.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/aahash.cpp [ 29% 7/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_data_stream.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_data_stream.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_data_stream.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/data_stream.cpp [ 33% 8/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_writer.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_writer.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_writer.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/seq_writer.cpp [ 37% 9/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_randseq.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_randseq.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_randseq.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/randseq.cpp [ 41% 10/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_process_pipeline.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_process_pipeline.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_process_pipeline.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/process_pipeline.cpp [ 45% 11/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_multiline_fastq_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_multiline_fastq_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_multiline_fastq_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/seq_reader_multiline_fastq_module.cpp [ 50% 12/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_util.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_util.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_util.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/util.cpp [ 54% 13/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_bloom_filter.cpp.o -MF 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 [ 58% 14/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_fastq_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_fastq_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_seq_reader_fastq_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/seq_reader_fastq_module.cpp [ 62% 15/24] 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_status.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_status.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_status.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/status.cpp [ 66% 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 --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 -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_cstring.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_cstring.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_src_btllib_cstring.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/src/btllib/cstring.cpp [ 70% 17/24] 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 -fstack-protector-strong -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 [ 75% 18/24] /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 [ 79% 19/24] c++ -Irecipes/indexlr.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/indexlr.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_indexlr.cpp.o -MF recipes/indexlr.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_indexlr.cpp.o.d -o recipes/indexlr.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_indexlr.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/recipes/indexlr.cpp [ 83% 20/24] 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 -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing '-Wl,-rpath,$ORIGIN/..:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/_build/ -Wl,-rpath-link,/usr/local/lib libbtllib.so -pthread -fopenmp /usr/local/lib/libsdsl.so /usr/local/lib/libdivsufsort.so /usr/local/lib/libdivsufsort64.so -Wl,--end-group [ 87% 21/24] c++ -Irecipes/randseq.p -Irecipes -I../recipes -Iinclude -I../include -I. -I.. -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I../subprojects/argparse/include -Isubprojects/argparse/__CMake_build -I../subprojects/argparse/__CMake_build -Isubprojects/argparse -I../subprojects/argparse -I/usr/local/include -fdiagnostics-color=never --coverage -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_FAST -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -pthread -MD -MQ recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_randseq.cpp.o -MF recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_randseq.cpp.o.d -o recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_randseq.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.5/recipes/randseq.cpp [ 91% 22/24] c++ -o recipes/randseq recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.5_recipes_randseq.cpp.o --coverage -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -ldl -lstdc++ -lm -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing '-Wl,-rpath,$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 -fstack-protector-strong -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=2025-05-02T23:01:36+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' '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 Sat May 3 00:06:07 BST 2025 build time: 00:04:36