=>> Building science/gemmi build started at Fri Mar 29 17:31:31 GMT 2024 port directory: /usr/ports/science/gemmi package name: gemmi-0.6.5 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 821 Feb 19 23:05 /usr/ports/science/gemmi/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 555deadfa3 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 08 ---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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(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 ===> gemmi-0.6.5 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 ===> gemmi-0.6.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gemmi-0.6.5 =========================================================================== =================================================== ===== 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 gemmi-0.6.5 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gemmi-0.6.5 for building => SHA256 Checksum OK for project-gemmi-gemmi-v0.6.5_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 gemmi-0.6.5 for building ===> Extracting for gemmi-0.6.5 => SHA256 Checksum OK for project-gemmi-gemmi-v0.6.5_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 gemmi-0.6.5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gemmi-0.6.5 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 ===> gemmi-0.6.5 depends on file: /usr/local/bin/cmake - found ===> Returning to build of gemmi-0.6.5 ===> gemmi-0.6.5 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 ===> gemmi-0.6.5 depends on executable: ninja - found ===> Returning to build of gemmi-0.6.5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for gemmi-0.6.5 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/science/gemmi/work/.build -- The C compiler identification is Clang 14.0.5 -- The CXX compiler identification is Clang 14.0.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /ccache/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: /ccache/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Gemmi version 0.6.5 -- Build type: Release -- Found ZLIB: /usr/lib/libz.so (found version "1.2.13") -- Benchmarks not configured. -- Skipping Python module. 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-- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/tao/pegtl/internal/duseltronik.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/tao/pegtl/internal/raise.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/tao/pegtl/internal/if_apply.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/tao/pegtl/internal/apply0.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/tao/pegtl/internal/rep_opt.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/tao/pegtl/internal/pad_opt.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/tao/pegtl/internal/lf_crlf_eol.hpp -- Installing: 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/wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/tao/pegtl/apply_mode.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/tinydir.h -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/pocketfft_hdronly.h -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/third_party/fast_float.h -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/bond_idx.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/fileutil.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/serialize.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/chemcomp.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/utf.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/atox.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/refln.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/align.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/addends.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/monlib.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/recgrid.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/json.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/fstream.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/calculate.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/elem.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/iterator.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/linkhunt.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/polyheur.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/twin.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/stats.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/mtz.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/small.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/to_mmcif.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/model.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/sprintf.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/floodfill.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/cif.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/unitcell.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/pdb_id.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/input.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/ddl.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/span.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/read_cif.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/reciproc.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/fail.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/read_map.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/asudata.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/formfact.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/grid.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/levmar.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/include/gemmi/qcp.hpp -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/lib/libgemmi_cpp.so -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/lib/cmake/gemmi/gemmi-targets.cmake -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/lib/cmake/gemmi/gemmi-targets-release.cmake -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/lib/cmake/gemmi/gemmi-config.cmake -- Installing: /wrkdirs/usr/ports/science/gemmi/work/stage/usr/local/lib/cmake/gemmi/gemmi-config-version.cmake ====> 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=2024-03-29T17:31:31+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=555deadfa3' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for gemmi-0.6.5 ===> Building gemmi-0.6.5 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for gemmi-0.6.5 build of science/gemmi | gemmi-0.6.5 ended at Fri Mar 29 17:49:38 GMT 2024 build time: 00:18:08