=>> Building biology/bamtools build started at Fri Mar 29 22:15:02 GMT 2024 port directory: /usr/ports/biology/bamtools package name: bamtools-2.5.2_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 401 Mar 8 2023 /usr/ports/biology/bamtools/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 01 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git 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-v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bamtools-2.5.2_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> bamtools-2.5.2_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bamtools-2.5.2_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bamtools-2.5.2_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bamtools-2.5.2_1 for building => SHA256 Checksum OK for pezmaster31-bamtools-v2.5.2_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bamtools-2.5.2_1 for building ===> Extracting for bamtools-2.5.2_1 => SHA256 Checksum OK for pezmaster31-bamtools-v2.5.2_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for bamtools-2.5.2_1 ===> Applying FreeBSD patches for bamtools-2.5.2_1 from /usr/ports/biology/bamtools/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bamtools-2.5.2_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.28.3... [pkg-builder.dan.net.uk] `-- Installing expat-2.6.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.5... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.5: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.48.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.48.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.28.3: .......... done ===> bamtools-2.5.2_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of bamtools-2.5.2_1 ===> bamtools-2.5.2_1 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,2.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,2... [pkg-builder.dan.net.uk] `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,2: ..... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> bamtools-2.5.2_1 depends on executable: ninja - found ===> Returning to build of bamtools-2.5.2_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bamtools-2.5.2_1 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-2.5.2_1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/bamtools/work/.build CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is Clang 14.0.5 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /ccache/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- 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 "1.2.13") -- 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 (1.5s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_CXX_FLAGS_DEBUG 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-2.5.2_1 [ 1% 1/62] /ccache/libexec/ccache/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/bamtools/work/bamtools-2.5.2/src -I/wrkdirs/usr/ports/biology/bamtools/work/.build/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o -MF src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o.d -o src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o -c /wrkdirs/usr/ports/biology/bamtools/work/bamtools-2.5.2/src/api/BamAlignment.cpp /wrkdirs/usr/ports/biology/bamtools/work/bamtools-2.5.2/src/api/BamAlignment.cpp:873:18: warning: variable 'newTagDataLength' set but not used [-Wunused-but-set-variable] unsigned int newTagDataLength = 0; ^ 1 warning generated. 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