From nobody Sun Feb 12 03:29:21 2023 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 4PDtHj59h9z3pD2Q for ; Sun, 12 Feb 2023 03:29:21 +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 4PDtHj21PXz4DGK for ; Sun, 12 Feb 2023 03:29:21 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1676172561; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=02myRDO54PVu2su3chdnRi8yH1r6TTVga8ZodRRfti8=; b=e8TSQAM6uenVK/89KXxS9Aq44T0ez0r47LrdiUPKxHkX30zsHSU9sGNa2u9al90q26W+j6 VGgQgMz0MvP8KRzYcIiQlE3ZfjRUch+3Y6wXcTFlAn0g8GWpdP2ZqyVQLoSwX2aIhxLBn9 ls8Sol6e8kOeF16SpU2fv1Zya8JF2Wsdfd5sGnn/3sLCye3y2S2NiBakywTt3DhC4h9KEl N9+X2AWrmfDuvm9VMSEvhcQ2qv9dljlcgAVIdn3OEGT/+h7Bo6gKy3YdVsPQRJnjMch+mY Bi7wJ8TGGBu/Z6DjUvkIFMaoq6sQ48q2wm8QQDEvDdzXDXdA3dSmq1JWXD7wSg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1676172561; a=rsa-sha256; cv=none; b=FcVm/SK4iPCS+VNmE/I12ngDq2LvYVSkk1JSG/bI+3b6iSDtZlWJtW2HdhNpAxnAao3u0A tbt2Eb7uvzvVmSQq1EJVQVoyuOjK/AWuWjtDef1Y7q1GqAIhzdaTWS2qRso/hDfgS8Tyvc vMoZ5LGLxS9wnXohwW5/zoYukurTXrXexSPCY1thgnzh/9f5EmQak9sqtMi5aYtv7SH5j0 3iIj8rTCOiOTPz7btdCFvoaEaX86KDSyi/dqLQt1C8PZ67yAPBIHJtaUN3MW/gZriUHwny 2WXyo3vqEiQp1mcCxOAzgY0Kq1LjZOCkR2mzKVMgb7o7NF3ntOYQogwVgL/myg== Received: from ampere3.nyi.freebsd.org (ampere3.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:26]) (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 did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4PDtHj13b7zNFj for ; Sun, 12 Feb 2023 03:29:21 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere3.nyi.freebsd.org (localhost [127.0.0.1]) by ampere3.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 31C3TL42047996 for ; Sun, 12 Feb 2023 03:29:21 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere3.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 31C3TLTZ047994; Sun, 12 Feb 2023 03:29:21 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sun, 12 Feb 2023 03:29:21 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202302120329.31C3TLTZ047994@ampere3.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 131releng-armv7-default][science/py-pymol] Failed for py39-pymol-2.5.0.97 in build X-ThisMailContainsUnwantedMimeParts: N 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/ampere3/data/131releng-armv7-default/96a5483c708f/logs/py39-pymol-2.5.0.97.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=131releng-armv7-default&build=96a5483c708f Log: =>> Building science/py-pymol build started at Sun Feb 12 03:27:25 UTC 2023 port directory: /usr/ports/science/py-pymol package name: py39-pymol-2.5.0.97 building for: FreeBSD 131releng-armv7-default-job-08 13.1-RELEASE-p5 FreeBSD 13.1-RELEASE-p5 1301000 arm maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1301000 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1301000 UNAME_v=FreeBSD 13.1-RELEASE-p5 1301000 UNAME_r=13.1-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 LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/131releng-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/131releng-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=131releng-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/131releng-armv7-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py39 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py39 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for py39-pymol-2.5.0.97: ====> GUI (Graphical User Interface) support: you have to select exactly one of them QT5=on: Qt 5 toolkit support TK=off: Tk GUI toolkit support ===> Use 'make config' to modify these settings ---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-pymol/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39/.cache HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-pymol/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-pymol/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39/.cache HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-pymol/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-pymol/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= LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST " MANPREFIX= "/usr/local" 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-- GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 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="" PYQT_APIDIR=share/PyQt5/3.9/qsci PYQT_DOCDIR=share/doc/PyQt5/3.9 PYQT_EXAMPLEDIR=share/examples/PyQt5/3.9 PYQT_SIPDIR=/usr/local/lib/python3.9/site-packages/PyQt5/bindings PYQT_DESIGNERDIR=/designer/PyQt5/3.9 PYQT_QMLDIR=/PyQt5/3.9 PYQT_SIPVERSION=6.7.2 PYQT_QSCIVERSION=2.13.3 PYQT_PYQTVERSION=5.15.7 OSREL=13.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py39-pymol" EXAMPLESDIR="share/examples/py39-pymol" DATADIR="share/py39-pymol" WWWDIR="www/py39-pymol" ETCDIR="etc/py39-pymol" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py39-pymol DOCSDIR=/usr/local/share/doc/py39-pymol EXAMPLESDIR=/usr/local/share/examples/py39-pymol WWWDIR=/usr/local/www/py39-pymol ETCDIR=/usr/local/etc/py39-pymol --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 #### /usr/local/etc/poudriere.d/make.conf #### # 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 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.1-RELEASE-p5 OSREL=13.1 OSVERSION=1301000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 1048576 stack size (kbytes, -s) 1048576 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) 1024 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-- =================================================== ===> License PyMOL accepted by the user =========================================================================== =================================================== ===> py39-pymol-2.5.0.97 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1.pkg [131releng-armv7-default-job-08] Installing pkg-1.19.1... [131releng-armv7-default-job-08] Extracting pkg-1.19.1: .......... done ===> py39-pymol-2.5.0.97 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-pymol-2.5.0.97 =========================================================================== =================================================== =========================================================================== =================================================== ===> License PyMOL accepted by the user ===> Fetching all distfiles required by py39-pymol-2.5.0.97 for building =========================================================================== =================================================== ===> License PyMOL accepted by the user ===> Fetching all distfiles required by py39-pymol-2.5.0.97 for building => SHA256 Checksum OK for schrodinger-pymol-open-source-v2.5.0-97-gd24468af_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License PyMOL accepted by the user ===> Fetching all distfiles required by py39-pymol-2.5.0.97 for building ===> Extracting for py39-pymol-2.5.0.97 => SHA256 Checksum OK for schrodinger-pymol-open-source-v2.5.0-97-gd24468af_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for py39-pymol-2.5.0.97 ===> Applying FreeBSD patches for py39-pymol-2.5.0.97 from /usr/ports/science/py-pymol/files =========================================================================== =================================================== ===> py39-pymol-2.5.0.97 depends on package: py39-numpy>=1.16,1<1.24,1 - not found ===> Installing existing package /packages/All/py39-numpy-1.23.5_2,1.pkg [131releng-armv7-default-job-08] Installing py39-numpy-1.23.5_2,1... [131releng-armv7-default-job-08] `-- Installing gcc12-12.2.0_5... [131releng-armv7-default-job-08] | `-- Installing binutils-2.39,1... [131releng-armv7-default-job-08] | | `-- Installing gettext-runtime-0.21.1... [131releng-armv7-default-job-08] | | `-- Installing indexinfo-0.3.1... [131releng-armv7-default-job-08] | | `-- Extracting indexinfo-0.3.1: .... done [131releng-armv7-default-job-08] | | `-- Extracting gettext-runtime-0.21.1: .......... done [131releng-armv7-default-job-08] | `-- Extracting binutils-2.39,1: .......... done c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Basis.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Basis.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/CGO.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/CGO.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/hash.c -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/hash.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/CGORenderer.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/CGORenderer.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 13 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Camera.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Camera.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Color.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Color.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Extrude.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Extrude.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/ContourSurf.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/ContourSurf.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/FontGLUT.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/FontGLUT.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/MyPNG.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/MyPNG.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 1 warning generated. 2 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/FontGLUT9x15.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/FontGLUT9x15.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer0/marching_cubes.cpp:21:10: fatal error: 'omp.h' file not found #include ^~~~~~~ 1 error generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/FontGLUTHel12.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/FontGLUTHel12.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 3 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Feedback.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/Feedback.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/FontType.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/FontType.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:1904:9: warning: unused variable 'last_ctnumber' [-Wunused-variable] int last_ctnumber = -1; ^ c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Ortho.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Ortho.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/FontGLUTHel10.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/FontGLUTHel10.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Vector.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/Vector.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/PConv.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/PConv.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/FontGLUTHel18.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/FontGLUTHel18.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/COLLADA.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/COLLADA.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/ShaderMgr.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/ShaderMgr.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Pop.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Pop.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Isosurf.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/Isosurf.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Match.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/Match.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Ray.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Ray.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Scene.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Scene.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 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-I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/SceneRender.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/SceneRender.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Character.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Character.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Tetsurf.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/Tetsurf.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML 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-I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/PyMOLObject.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/PyMOLObject.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/ScrollBar.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/ScrollBar.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/ButMode.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/ButMode.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST 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-I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/ccealignmodule.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/ccealignmodule.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/SymOp.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/SymOp.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Sphere.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/Sphere.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN 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-I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/FontGLUT8x13.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/FontGLUT8x13.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/SymOpTools.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/SymOpTools.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Deferred.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/Deferred.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Text.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Text.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/SymOpPConv.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/SymOpPConv.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Tracker.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer0/Tracker.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/View.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/View.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Picking.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Picking.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/AssemblyHelpers.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/AssemblyHelpers.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Movie.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Movie.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/AtomInfoHistory.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/AtomInfoHistory.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/CifFile.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/CifFile.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/CoordSet.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/CoordSet.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/GadgetSet.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/GadgetSet.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/MmodTyping.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/MmodTyping.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/Mol2Typing.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/Mol2Typing.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Seq.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Seq.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectAlignment.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectAlignment.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/SceneRay.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/SceneRay.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Font.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Font.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectCallback.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectCallback.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/SceneView.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/SceneView.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/MmtfMoleculeReader.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/MmtfMoleculeReader.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectGadget.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectGadget.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/BondTypeHistory.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/BondTypeHistory.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectGroup.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectGroup.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectMesh.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectMesh.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectMolecule2.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectMolecule2.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer2/ObjectMolecule2.cpp:20:10: fatal error: 'omp.h' file not found #include ^~~~~~~ c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectSlice.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectSlice.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectVolume.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectVolume.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Wizard.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Wizard.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Symmetry.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Symmetry.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepCartoon.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepCartoon.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/P.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/P.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/AtomInfo.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/AtomInfo.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepDihedral.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepDihedral.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepDistLabel.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepDistLabel.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepEllipsoid.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepEllipsoid.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepMesh.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepMesh.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/CifMoleculeReader.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/CifMoleculeReader.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/MolV3000.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/MolV3000.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/HydrogenAdder.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/HydrogenAdder.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepNonbondedSphere.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepNonbondedSphere.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Control.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Control.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer2/MmtfMoleculeReader.cpp:171:18: warning: address of array 'container->unitCell' will always evaluate to 'true' [-Wpointer-bool-conversion] if (container->unitCell && ~~~~~~~~~~~^~~~~~~~ ~~ c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectMap.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectMap.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/SceneMouse.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/SceneMouse.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/DistSet.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/DistSet.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectDist.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectDist.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectGadgetRamp.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectGadgetRamp.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepSphere.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepSphere.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepSphereImmediate.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepSphereImmediate.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectMolecule2.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectMolecule2.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 1. parser at end of file #0 0x03c83de4 (/usr/bin/c+++0x3c83de4) #1 0x03c81d70 (/usr/bin/c+++0x3c81d70) #2 0x03c2220c (/usr/bin/c+++0x3c2220c) #3 0x450ec12c (/lib/libthr.so.3+0x2712c) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Rep.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Rep.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepWireBond.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepWireBond.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/SculptCache.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/SculptCache.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++: note: diagnostic msg: Error generating preprocessed source(s). c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/VFont.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/VFont.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/CifDataValueFormatter.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/CifDataValueFormatter.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepLabel.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepLabel.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepDistDash.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepDistDash.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/SideChainHelper.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/SideChainHelper.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectCGO.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectCGO.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/Editor.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/Editor.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepDot.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepDot.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/Executive.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/Executive.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/MaeExportHelpers.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/MaeExportHelpers.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/MovieScene.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/MovieScene.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectMolecule.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectMolecule.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectSurface.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/ObjectSurface.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/RingFinder.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/RingFinder.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer3/Executive.cpp:31:10: fatal error: 'omp.h' file not found #include ^~~~~~~ c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/Selector.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/Selector.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepRibbon.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepRibbon.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepNonbonded.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepNonbonded.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/SpecRec.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/SpecRec.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepAngle.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepAngle.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepSurface.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepSurface.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer4/Cmd.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer4/Cmd.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer4/PopUp.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer4/PopUp.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepSphereGenerate.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepSphereGenerate.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer5/TestPyMOL.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer5/TestPyMOL.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD ov/src/OVContext.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/ov/src/OVContext.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/AtomIterators.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/AtomIterators.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/Executive.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/Executive.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 1. parser at end of file #0 0x03c83de4 (/usr/bin/c+++0x3c83de4) #1 0x03c81d70 (/usr/bin/c+++0x3c81d70) #2 0x03c2220c (/usr/bin/c+++0x3c2220c) #3 0x450ec12c (/lib/libthr.so.3+0x2712c) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD ov/src/OVHeapArray.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/ov/src/OVHeapArray.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD ov/src/OVHeap.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/ov/src/OVHeap.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/Sculpt.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/Sculpt.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD ov/src/OVLexicon.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/ov/src/OVLexicon.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD ov/src/OVOneToAny.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/ov/src/OVOneToAny.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD ov/src/OVOneToOne.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/ov/src/OVOneToOne.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD ov/src/OVRandom.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/ov/src/OVRandom.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD ov/src/ov_utility.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/ov/src/ov_utility.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/MoleculeExporter.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/MoleculeExporter.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++: note: diagnostic msg: Error generating preprocessed source(s). c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/Seeker.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/Seeker.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/RepCylBond.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer2/RepCylBond.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/SpecRecSpecial.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/SpecRecSpecial.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer5/PyMOL.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer5/PyMOL.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer5/main.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer5/main.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/CGOGL.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/CGOGL.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/PlugIOManager.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/PlugIOManager.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer4/Menu.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer4/Menu.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/TypeFace.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/TypeFace.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/SelectorTmp.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer3/SelectorTmp.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Shaker.cpp -o build/temp.freebsd-13.1-RELEASE-p5-arm-cpython-39/layer1/Shaker.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp error: command '/usr/bin/c++' failed with exit code 1 *** Error code 1 Stop. make: stopped in /usr/ports/science/py-pymol