From nobody Sat Mar 30 05:16:56 2024 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4V659k0BpDz5GCRr for ; Sat, 30 Mar 2024 05:16:58 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4V659j2G2jz4FdF for ; Sat, 30 Mar 2024 05:16:57 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1711775817; a=rsa-sha256; cv=none; b=asp3VsN7moKFr/sW4F/Iw2wL0170Aq7/NJb5aYT2vYW2JZ6mz5DzyMrX3saejtB1AvPHyd g8EyLHavguI16LoMPg380iSB8tUmiKB/w7L94Q8wSXlWRuyTcmm8haTamW0cjWiz4ivuEw eDU+V0b7ydrn+2033yGrr2e2vogC21qF1vADUzevJO1pk7K6/AT1AJEMt6p9FtqzYmxhE8 dRSZk91vw0UIivLpSflbjU1bol4EMJL/pW3EqITWonzn9cB5ci9Uwlv7JZ5ABKR3cN4xn8 ed9MXQaRPqStMRlDS6SqNAbD2pxzaQAGn/8qw1A5uNOJdk+0A34/2zNoH/nm6A== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1711775817; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=MLClUV54DIcHo2GQILOimujjZFf/ClAV36Or7Q479kY=; b=EvhaxddskjUtqtL0p+vvCYbCfCyhpAlMQdMK1erNXcIACVhRXD+6SXMhEnhoBP9RpC/0Ze IUbE/Nhz9WUW19dNu3cWn0sow3iOJF2aPvILL8cEXqlRMmSqm+PicGTWX+SeItFc7gdGE5 uPlOLin3aIUr2vqkxD8vKt/NHGSEQaV84fqnf2Ovst8BBzQOV5EMRHK/OJpYzGhmFUhmgx gHA+QSVdbeXR9wS/bkRh97bfSUJ735NfmSGWJDHYbd9RL92CUedsM29Z+vgHzGhb+XuR5b UUMCtddMU2TJiYJjY8oB39otlBg5DDz96n2ZwKbUhIAtn/tDKaxK3Xj1Bao4iA== Received: from package19.nyi.freebsd.org (package19.nyi.freebsd.org [IPv6:2610:1c1:1:607e::16:7]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4V659j0Cnszh0H for ; Sat, 30 Mar 2024 05:16:57 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 41ca by package19.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on package19.nyi.freebsd.org); Sat, 30 Mar 2024 05:16:56 +0000 To: yuri@FreeBSD.org Subject: [exp - 140amd64-default-build-as-user][science/py-MDAnalysis] Failed for py39-MDAnalysis-2.3.0_1 in build Cc: pkg-fallout@FreeBSD.org Date: Sat, 30 Mar 2024 05:16:56 +0000 Message-Id: <6607a048.41ca.6dff876b@package19.nyi.freebsd.org> From: List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/package19/data/140amd64-default-build-as-user/fc7786a84279/logs/py39-MDAnalysis-2.3.0_1.log Build URL: https://pkg-status.freebsd.org/package19/build.html?mastername=140amd64-default-build-as-user&build=fc7786a84279 Log: =>> Building science/py-MDAnalysis build started at Sat Mar 30 05:15:31 UTC 2024 port directory: /usr/ports/science/py-MDAnalysis package name: py39-MDAnalysis-2.3.0_1 building for: FreeBSD 140amd64-default-build-as-user-job-09 14.0-RELEASE-p5 FreeBSD 14.0-RELEASE-p5 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1507 Jun 29 2023 /usr/ports/science/py-MDAnalysis/Makefile Ports top last git commit: fc7786a8427 Ports top unclean checkout: no Port dir last git commit: 3d9a815d9c5 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.1-1-g1e9f97d6 Host OSVERSION: 1500006 Jail OSVERSION: 1400097 Job Id: 09 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400097 UNAME_v=FreeBSD 14.0-RELEASE-p5 UNAME_r=14.0-RELEASE-p5 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=3.4.1-1-g1e9f97d6 MASTERMNT=/poudriere/data/.m/140amd64-default-build-as-user/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/poudriere/data/.m/140amd64-default-build-as-user/09/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=140amd64-default-build-as-user SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/poudriere/data/.m/140amd64-default-build-as-user/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.1-1-g1e9f97d6 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py39 MAKE_ARGS= FLAVOR=py39 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/.cache HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/.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-py39/.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-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/.cache HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/.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-py39/.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 -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="ins tall -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/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=14.0 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/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 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 FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---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 --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-MDAnalysis-2.3.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [140amd64-default-build-as-user-job-09] Installing pkg-1.20.9_1... [140amd64-default-build-as-user-job-09] Extracting pkg-1.20.9_1: .......... done ===> py39-MDAnalysis-2.3.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-MDAnalysis-2.3.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py39-MDAnalysis-2.3.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py39-MDAnalysis-2.3.0_1 for building => SHA256 Checksum OK for MDAnalysis-2.3.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py39-MDAnalysis-2.3.0_1 for building ===> Extracting for py39-MDAnalysis-2.3.0_1 => SHA256 Checksum OK for MDAnalysis-2.3.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for py39-MDAnalysis-2.3.0_1 ===> Applying FreeBSD patches for py39-MDAnalysis-2.3.0_1 from /usr/ports/science/py-MDAnalysis/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-MDAnalysis-2.3.0_1 depends on package: py39-numpy>=1.16,1<1.26,1 - not found ===> Installing existing package /packages/All/py39-numpy-1.25.0_6,1.pkg [140amd64-default-build-as-user-job-09] Installing py39-numpy-1.25.0_6,1... [140amd64-default-build-as-user-job-09] `-- Installing gcc13-13.2.0_4... [140amd64-default-build-as-user-job-09] | `-- Installing binutils-2.40_5,1... [140amd64-default-build-as-user-job-09] | | `-- Installing gettext-runtime-0.22.5... [140amd64-default-build-as-user-job-09] | | `-- Installing indexinfo-0.3.1... [140amd64-default-build-as-user-job-09] | | `-- Extracting indexinfo-0.3.1: .... done [140amd64-default-build-as-user-job-09] | | `-- Extracting gettext-runtime-0.22.5: .......... done [140amd64-default-build-as-user-job-09] | | `-- Installing zstd-1.5.5_1... [140amd64-default-build-as-user-job-09] | | `-- Installing liblz4-1.9.4_1,1... [140amd64-default-build-as-user-job-09] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [140amd64-default-build-as-user-job-09] | | `-- Extracting zstd-1.5.5_1: .......... done [140amd64-default-build-as-user-job-09] | `-- Extracting binutils-2.40_5,1: .......... done [140amd64-default-build-as-user-job-09] | `-- Installing gmp-6.3.0... [140amd64-default-build-as-user-job-09] | `-- Extracting gmp-6.3.0: .......... done [140amd64-default-build-as-user-job-09] | `-- Installing mpc-1.3.1_1... [140amd64-default-build-as-user-job-09] | | `-- Installing mpfr-4.2.1,1... [140amd64-default-build-as-user-job-09] | | `-- Extracting mpfr-4.2.1,1: .......... done [140amd64-default-build-as-user-job-09] | `-- Extracting mpc-1.3.1_1: ......... done [140amd64-default-build-as-user-job-09] `-- Extracting gcc13-13.2.0_4: .......... done [140amd64-default-build-as-user-job-09] `-- Installing openblas-0.3.25,2... [140amd64-default-build-as-user-job-09] `-- Extracting openblas-0.3.25,2: .......... done [140amd64-default-build-as-user-job-09] `-- Installing py39-setuptools-63.1.0_1... [140amd64-default-build-as-user-job-09] | `-- Installing python39-3.9.18_2... [140amd64-default-build-as-user-job-09] | | `-- Installing libffi-3.4.4_1... [140amd64-default-build-as-user-job-09] | | `-- Extracting libffi-3.4.4_1: .......... done [140amd64-default-build-as-user-job-09] | | `-- Installing mpdecimal-4.0.0... [140amd64-default-build-as-user-job-09] | | `-- Extracting mpdecimal-4.0.0: .......... done [140amd64-default-build-as-user-job-09] | | `-- Installing readline-8.2.10... #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ 3 warnings generated. cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -o build/lib.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/c_distances.cpython-39.so building 'MDAnalysis.lib.c_distances_openmp' extension cc -Wno-unused-result -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/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/include -I/usr/local/include/python3.9 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/c_distances_openmp.c:797: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ 1 warning generated. cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -o build/lib.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/c_distances_openmp.cpython-39.so -fopenmp building 'MDAnalysis.lib.qcprot' extension cc -Wno-unused-result -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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MDAnalysis/lib/qcprot.c -o build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/qcprot.c:780: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ MDAnalysis/lib/qcprot.c:2385:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:2593:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { ~~~~~~~~~ ^ ~~~~~~~~~ 3 warnings generated. cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/qcprot.o -L/usr/local/lib -o build/lib.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/qcprot.cpython-39.so building 'MDAnalysis.lib._transformations' extension creating build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/src creating build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/src/transformations cc -Wno-unused-result -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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/src/transformations/transformations.c:73: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ MDAnalysis/lib/src/transformations/transformations.c:2122:35: warning: 'PyUnicode_GetSize' is deprecated [-Wdeprecated-declarations] if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { ^ /usr/local/include/python3.9/unicodeobject.h:177:1: note: 'PyUnicode_GetSize' has been explicitly marked deprecated here Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( ^ /usr/local/include/python3.9/pyport.h:508:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ 2 warnings generated. cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -o build/lib.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/_transformations.cpython-39.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/formats/src cc -Wno-unused-result -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-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/include/python3.9 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/libmdaxdr.c:807: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ In file included from MDAnalysis/lib/formats/libmdaxdr.c:816: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- ^ In file included from MDAnalysis/lib/formats/libmdaxdr.c:817: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: '/*' within block comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- ^ In file included from MDAnalysis/lib/formats/libmdaxdr.c:818: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- ^ MDAnalysis/lib/formats/libmdaxdr.c:28469:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ MDAnalysis/lib/formats/libmdaxdr.c:400:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ MDAnalysis/lib/formats/libmdaxdr.c:28480:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ MDAnalysis/lib/formats/libmdaxdr.c:400:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ MDAnalysis/lib/formats/libmdaxdr.c:29345:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ MDAnalysis/lib/formats/libmdaxdr.c:400:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ MDAnalysis/lib/formats/libmdaxdr.c:29356:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ MDAnalysis/lib/formats/libmdaxdr.c:400:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ 8 warnings generated. cc -Wno-unused-result -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-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/include/python3.9 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] /* -*- 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-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- ^ 2 warnings generated. cc -Wno-unused-result -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-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] /* -*- 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] 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] 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] 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] 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] 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] 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] 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] maxidx = (LASTIDXxfp->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] (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] (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] 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] 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] maxidx = (LASTIDXxfp->buf1size) ~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] maxidx = (LASTIDXxfp->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] (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] (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] 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] 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] maxidx = (LASTIDX