=>> Building biology/bamtools build started at Wed Mar 11 04:02:45 EDT 2026 port directory: /usr/ports/biology/bamtools package name: bamtools-2.5.3 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 424 Jun 29 2025 /usr/ports/biology/bamtools/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: 101f13edbc07 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 13 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/13/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bamtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bamtools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bamtools/work/.cache HOME=/wrkdirs/usr/ports/biology/bamtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bamtools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bamtools/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/bamtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bamtools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bamtools/work/.cache HOME=/wrkdirs/usr/ports/biology/bamtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bamtools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bamtools/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/bamtools/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-- PORTVERSION=2.5.3 CMAKE_BUILD_TYPE="release" OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bamtools" EXAMPLESDIR="share/examples/bamtools" DATADIR="share/bamtools" WWWDIR="www/bamtools" ETCDIR="etc/bamtools" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bamtools DOCSDIR=/usr/local/share/doc/bamtools EXAMPLESDIR=/usr/local/share/examples/bamtools WWWDIR=/usr/local/www/bamtools ETCDIR=/usr/local/etc/bamtools --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 ===> bamtools-2.5.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> bamtools-2.5.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bamtools-2.5.3 =========================================================================== =================================================== ===== 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 bamtools-2.5.3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bamtools-2.5.3 for building => SHA256 Checksum OK for pezmaster31-bamtools-v2.5.3_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 bamtools-2.5.3 for building ===> Extracting for bamtools-2.5.3 => SHA256 Checksum OK for pezmaster31-bamtools-v2.5.3_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 bamtools-2.5.3 ===> Applying FreeBSD patches for bamtools-2.5.3 from /usr/ports/biology/bamtools/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bamtools-2.5.3 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.10_1.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.10_1... [pkg.DaveG.ca] `-- Installing expat-2.7.4... [pkg.DaveG.ca] `-- Extracting expat-2.7.4: .......... done [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Installing libunistring-1.4.2... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.2: .......... done [pkg.DaveG.ca] `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.52.0... [pkg.DaveG.ca] `-- Extracting libuv-1.52.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.6... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] `-- Extracting rhash-1.4.6: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.10_1: .......... done ===> bamtools-2.5.3 depends on file: /usr/local/bin/cmake - found ===> Returning to build of bamtools-2.5.3 ===> bamtools-2.5.3 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.13.2,4.pkg [pkg.DaveG.ca] Installing ninja-1.13.2,4... [pkg.DaveG.ca] `-- Installing python311-3.11.15... [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-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.15: .......... done [pkg.DaveG.ca] Extracting ninja-1.13.2,4: ..... done ===== Message from python311-3.11.15: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> bamtools-2.5.3 depends on executable: ninja - found ===> Returning to build of bamtools-2.5.3 ===> bamtools-2.5.3 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. ===> bamtools-2.5.3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of bamtools-2.5.3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bamtools-2.5.3 depends on shared library: libjsoncpp.so - found (/usr/local/lib/libjsoncpp.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for bamtools-2.5.3 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/bamtools/work/.build -- 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 -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) -- Checking for one of the modules 'jsoncpp>=1' Did NOT find system JsonCpp, instead using bundled version -- Found ZLIB: /usr/lib/libz.so (found version "1.3.1") -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done (10.0s) -- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_COMPILER CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/bamtools/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for bamtools-2.5.3 [ 1% 57/62] /usr/local/libexec/ccache/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/bamtools/work/bamtools-2.5.3/src 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=================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for bamtools-2.5.3 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/biology/bamtools/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/lib/libbamtools.so.2.5.3 -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/lib/libbamtools.so -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/bin/bamtools -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/bin/bamtools" to "" -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamAlgorithms.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamAlignment.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamAux.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamConstants.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamIndex.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamMultiReader.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamReader.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamWriter.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/IBamIODevice.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamConstants.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamHeader.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamProgram.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamProgramChain.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamReadGroup.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamReadGroupDictionary.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamSequence.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamSequenceDictionary.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/api_global.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/bamtools_api_export.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/api/algorithms/Sort.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/include/bamtools/shared/bamtools_global.h -- Installing: /wrkdirs/usr/ports/biology/bamtools/work/stage/usr/local/lib/pkgconfig/bamtools-1.pc ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-03-11T08:02:45+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=101f13edbc07' '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 bamtools-2.5.3 ===> Building bamtools-2.5.3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for bamtools-2.5.3 build of biology/bamtools | bamtools-2.5.3 ended at Wed Mar 11 04:04:08 EDT 2026 build time: 00:01:27