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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy23/data/150amd64-default/46e799e2bb66/logs/py311-MDAnalysis-2.10.0_1.log Build URL: https://pkg-status.freebsd.org/beefy23/build.html?mastername=150amd64-default&build=46e799e2bb66 Log: =>> Building science/py-MDAnalysis build started at Sat May 16 02:32:49 UTC 2026 port directory: /usr/ports/science/py-MDAnalysis package name: py311-MDAnalysis-2.10.0_1 building for: FreeBSD 150amd64-default-job-02 15.0-RELEASE-p8 FreeBSD 15.0-RELEASE-p8 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 1616 May 7 01:01 /usr/ports/science/py-MDAnalysis/Makefile Ports top last git commit: 46e799e2bb66d287ebca2fefa984cb842ba36f5c Ports top unclean checkout: no Port dir last git commit: 2bf3834a197ccf8956332378eda8dd7577965246 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8 Host OSVERSION: 1600018 Jail OSVERSION: 1500068 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p8 UNAME_r=15.0-RELEASE-p8 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=3.4.8 MASTERMNT=/usr/local/poudriere/data/.m/150amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/150amd64-default/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=150amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/150amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.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 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -s " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/MDAnalysis" EXAMPLESDIR="share/examples/MDAnalysis" DATADIR="share/MDAnalysis" WWWDIR="www/MDAnalysis" ETCDIR="etc/MDAnalysis" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/MDAnalysis DOCSDIR=/usr/local/share/doc/MDAnalysis EXAMPLESDIR=/usr/local/share/examples/MDAnalysis WWWDIR=/usr/local/www/MDAnalysis ETCDIR=/usr/local/etc/MDAnalysis --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### 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-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-MDAnalysis-2.10.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [150amd64-default-job-02] Installing pkg-2.7.5... [150amd64-default-job-02] Extracting pkg-2.7.5: .......... done ===> py311-MDAnalysis-2.10.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-MDAnalysis-2.10.0_1 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py311-MDAnalysis-2.10.0_1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py311-MDAnalysis-2.10.0_1 for building => SHA256 Checksum OK for mdanalysis-2.10.0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py311-MDAnalysis-2.10.0_1 for building ===> Extracting for py311-MDAnalysis-2.10.0_1 => SHA256 Checksum OK for mdanalysis-2.10.0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py311-MDAnalysis-2.10.0_1 ===> Applying FreeBSD patches for py311-MDAnalysis-2.10.0_1 from /usr/ports/science/py-MDAnalysis/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-MDAnalysis-2.10.0_1 depends on package: py311-cython>=0.28 - not found ===> Installing existing package /packages/All/py311-cython-3.2.4.pkg [150amd64-default-job-02] Installing py311-cython-3.2.4... [150amd64-default-job-02] `-- Installing python311-3.11.15_2... [150amd64-default-job-02] | `-- Installing gettext-runtime-1.0_1... [150amd64-default-job-02] | | `-- Installing indexinfo-0.3.1_1... [150amd64-default-job-02] | | `-- Extracting indexinfo-0.3.1_1: .... done [150amd64-default-job-02] | `-- Extracting gettext-runtime-1.0_1: .......... done [150amd64-default-job-02] | `-- Installing libffi-3.5.1... [150amd64-default-job-02] | `-- Extracting libffi-3.5.1: .......... done [150amd64-default-job-02] | `-- Installing mpdecimal-4.0.1... [150amd64-default-job-02] | `-- Extracting mpdecimal-4.0.1: .......... done [150amd64-default-job-02] | `-- Installing readline-8.3.3... [150amd64-default-job-02] | `-- Extracting readline-8.3.3: .......... done [150amd64-default-job-02] `-- Extracting python311-3.11.15_2: .......... done [150amd64-default-job-02] Extracting py311-cython-3.2.4: .......... done ===== Message from python311-3.11.15_2: -- 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 <snip> copying doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/IMD.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TPR.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/coordinates creating build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/converters creating build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/auxiliary creating build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/analysis/legacy copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/analysis/legacy creating build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/analysis/encore creating build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/doc/sphinx/source/documentation_pages/lib/formats running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311 creating build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis creating build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib creating build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/formats cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.o -std=c11 -O3 -funroll-loops -fsigned-zeros cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.o -L/usr/local/lib -o build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.cpython-311.so building 'MDAnalysis.lib.c_distances' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/c_distances.c -o build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/c_distances.o -std=c11 -O3 -funroll-loops -fsigned-zeros cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -o build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/c_distances.cpython-311.so building 'MDAnalysis.lib.c_distances_openmp' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -DPARALLEL -I/usr/local/lib/python3.11/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c11 -O3 -funroll-loops -fsigned-zeros cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -o build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/c_distances_openmp.cpython-311.so -fopenmp building 'MDAnalysis.lib.qcprot' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/_core/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/qcprot.c -o build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/qcprot.o -std=c11 -O3 -funroll-loops -fsigned-zeros MDAnalysis/lib/qcprot.c:21294:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 21294 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:21502:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 21502 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:21933:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 21933 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:22141:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 22141 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ 4 warnings generated. cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/qcprot.o -L/usr/local/lib -o build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/qcprot.cpython-311.so building 'MDAnalysis.lib._transformations' extension creating build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/src creating build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/src/transformations cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/_core/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/src/transformations/transformations.o -std=c11 -O3 -funroll-loops -fsigned-zeros cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -o build/lib.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/_transformations.cpython-311.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/formats/src cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/libmdaxdr.c:1186: MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from MDAnalysis/lib/formats/libmdaxdr.c:1187: MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from MDAnalysis/lib/formats/libmdaxdr.c:1188: MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ 3 warnings generated. cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/formats/src/trr_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ 2 warnings generated. cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.freebsd-15.0-RELEASE-p8-amd64-cpython-311/MDAnalysis/lib/formats/src/xdrfile.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] 501 | while (size >= num && num_of_bits < 32) | ~~~~ ^ ~~~ MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 547 | while (bytes[num_of_bytes] >= num) | ~~~~~~~~~~~~~~~~~~~ ^ ~~~ MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] 656 | if (num_of_bits >= num_of_bytes * 8) | ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] 658 | for (i = 0; i < num_of_bytes; i++) | ~ ^ ~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] 666 | for (i = 0; i < num_of_bytes-1; i++) | ~ ^ ~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 706 | if (lastbits < num_of_bits) | ~~~~~~~~ ^ ~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 816 | if(size3>xfp->buf1size) | ~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] 868 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp; | ~~~~~~~^~~~ MDAnalysis/lib/formats/src/xdrfile.c:1012:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 1012 | if(size3>xfp->buf1size) | ~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1109:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1109 | (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1108:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1108 | (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1107:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1107 | if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) | ~~~~~~~~ ^ ~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] 1141 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp; | ~~~~~~~^~~~ MDAnalysis/lib/formats/src/xdrfile.c:1273:8: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] 1273 | if(tmp==(unsigned int)buf2[0]) | ~~~^ ~~~~~~~~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1313:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 1313 | if(size3>xfp->buf1size) | ~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] 1368 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp; | ~~~~~~~^~~~ MDAnalysis/lib/formats/src/xdrfile.c:1504:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 1504 | if(size3>xfp->buf1size) { | ~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1596:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1596 | (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1595:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1595 | (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1594:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1594 | if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { | ~~~~~~~~ ^ ~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] 1624 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp; | ~~~~~~~^~~~ MDAnalysis/lib/formats/src/xdrfile.c:1734:8: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] 1734 | if(tmp==(unsigned int)buf2[0]) | ~~~^ ~~~~~~~~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:2536:3: error: incompatible function pointer types initializing 'off_t (*)(XDR *, off_t, int)' (aka 'long (*)(struct XDR *, long, int)') with an expression of type 'int (XDR *, int64_t, int)' (aka 'int (struct XDR *, long, int)') [-Wincompatible-function-pointer-types] 2536 | xdrstdio_setpos, /* set offset in the stream */ | ^~~~~~~~~~~~~~~ 25 warnings and 1 error generated. error: command '/usr/bin/cc' failed with exit code 1 *** Error code 1 Stop. make: stopped making "build" in /usr/ports/science/py-MDAnalysis
