From nobody Wed Nov 16 02:05:27 2022 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 4NBmbX5BKGz4hCC2 for ; Wed, 16 Nov 2022 02:05:28 +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 4NBmbX1CNMz3tWv; Wed, 16 Nov 2022 02:05:28 +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=1668564328; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=P6fl9pYufeNPwvxUqWeZgen93hhCMrPCMgNUtqOX210=; b=pNsPC4gN4XFTJrISpPX5XhSe0KB1G8QtWE7HQn3TQiq3ErnDTiwBZ0BpY+08GDr3m9ezsv rQkcYguMPuD/WjUXrrEDM8RPOBz/CDXZ+4vY+3cvwY0JTF0XOBhrTQWh/m3bCzh3zShore PKCebr36uQcSOq6xwVkaud8N82YmRRiBbx/O/aHhSSFdXf3QLW5buyFU5/+6xwLbosS5PA hge2LL6GVWugNntSHhaeP3HkGOfm/jM6IovJcu/MCrbMuPqwRw8yD+AxBdI2x8IwxCUpxV ILx9fjv2AnAU4CCSm8jZtgziMPrRRkCu80+QhDCUb99OWh/QPAjsmsXIOLNOpg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1668564328; a=rsa-sha256; cv=none; b=aXHEDow6uRT1IFQNp6As1/pgDSO9n8wBAXJwlPaCdusITPedtpB74mk0BfmkYR4b7vmc2H LoAoSae2ZenId8su/QXPm12DfyHITDljRTx4/aC4+4GX8P/15oZPLVhSIfTwN/STsDJzee s87jlhiCdgB+66f9Q5LpSyYKPtVRqoysqQ60ZmB0GmJhgpywngnxngbhaM+9KD3uZfgwl7 Q2Re1MEW+hXBnsSRWmzZ4QeJcgAypj2tjC1LaElyYPw5FS6kV5HkXunNNYBtoUBlVShlDE TdVtZTDVXq7DwN2vFYMuYdEgpCg8+s7mp3xB8Uqdx3MwMEihdJRsizroNF3DeA== Received: from beefy15.nyi.freebsd.org (beefy15.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:1e]) (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 4NBmbX0Ct0zktK; Wed, 16 Nov 2022 02:05:28 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy15.nyi.freebsd.org (localhost [127.0.0.1]) by beefy15.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 2AG25R9q098424; Wed, 16 Nov 2022 02:05:27 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy15.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 2AG25RdO098421; Wed, 16 Nov 2022 02:05:27 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 16 Nov 2022 02:05:27 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202211160205.2AG25RdO098421@beefy15.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - 131i386-default][science/py-pymol] Failed for py39-pymol-2.4.0_7 in build Cc: pkg-fallout@FreeBSD.org 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/beefy15/data/131i386-default/387f99b7180f/logs/py39-pymol-2.4.0_7.log Build URL: https://pkg-status.freebsd.org/beefy15/build.html?mastername=131i386-default&build=387f99b7180f Log: =>> Building science/py-pymol build started at Wed Nov 16 02:04:19 UTC 2022 port directory: /usr/ports/science/py-pymol package name: py39-pymol-2.4.0_7 building for: FreeBSD 131i386-default-job-06 13.1-RELEASE-p3 FreeBSD 13.1-RELEASE-p3 i386 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1301000 Job Id: 06 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1301000 UNAME_v=FreeBSD 13.1-RELEASE-p3 UNAME_r=13.1-RELEASE-p3 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/131i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/131i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=131i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/131i386-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-2.4.0_7: ====> 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 " MANPREFIX="/usr/local" BSD_IN STALL_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 MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /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: i386-unknown-freebsd13.1 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: i386-unknown-freebsd13.1 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" "-m" "elf_i386_fbsd" "-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: i386-unknown-freebsd13.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=13.1-RELEASE-p3 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) 524288 stack size (kbytes, -s) 65536 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-2.4.0_7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.18.4.pkg [131i386-default-job-06] Installing pkg-1.18.4... [131i386-default-job-06] Extracting pkg-1.18.4: .......... done ===> py39-pymol-2.4.0_7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-pymol-2.4.0_7 =========================================================================== =================================================== =========================================================================== =================================================== ===> License PyMOL accepted by the user ===> Fetching all distfiles required by py39-pymol-2.4.0_7 for building =========================================================================== =================================================== ===> License PyMOL accepted by the user ===> Fetching all distfiles required by py39-pymol-2.4.0_7 for building => SHA256 Checksum OK for schrodinger-pymol-open-source-v2.4.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License PyMOL accepted by the user ===> Fetching all distfiles required by py39-pymol-2.4.0_7 for building ===> Extracting for py39-pymol-2.4.0_7 => SHA256 Checksum OK for schrodinger-pymol-open-source-v2.4.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for py39-pymol-2.4.0_7 ===> Applying FreeBSD patches for py39-pymol-2.4.0_7 from /usr/ports/science/py-pymol/files =========================================================================== =================================================== ===> py39-pymol-2.4.0_7 depends on package: py39-numpy>=1.16,1<1.24,1 - not found ===> Installing existing package /packages/All/py39-numpy-1.23.4,1.pkg [131i386-default-job-06] Installing py39-numpy-1.23.4,1... [131i386-default-job-06] `-- Installing gcc11-11.3.0_5... [131i386-default-job-06] | `-- Installing binutils-2.39,1... In file included from 1 warning generated. layer3/AtomIterators.cpp:9: In file included from layer3/AtomIterators.h:11: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer5/PyMOL.cpp:32: In file included from layer3/Selector.h:24: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer3/Seeker.cpp:27: In file included from layer3/Seeker.h:21: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -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-p3-i386-cpython-39/layer2/CoordSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. In file included from 1 error generated. layer2/RepCylBond.cpp:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. layer5/PyMOL.cpp:1798:3: warning: 'PyEval_InitThreads' is deprecated [-Wdeprecated-declarations] PyEval_InitThreads(); ^ /usr/local/include/python3.9/ceval.h:130:1: note: 'PyEval_InitThreads' has been explicitly marked deprecated here Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); ^ /usr/local/include/python3.9/pyport.h:508:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -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-p3-i386-cpython-39/layer3/PlugIOManager.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -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-p3-i386-cpython-39/layer2/ObjectMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -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-p3-i386-cpython-39/ov/src/OVContext.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer5/main.cpp:45: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -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-p3-i386-cpython-39/layer2/ObjectMolecule2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. 1 warning generated. 2 warnings generated. 1 warning generated. In file included from layer3/PlugIOManager.cpp:24: In file included from layer3/PlugIOManager.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/CoordSet.cpp:29: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. In file included from layer2/ObjectMesh.cpp:35: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/ObjectMolecule2.cpp:31: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. 1 warning generated. 1 warning generated. 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -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-p3-i386-cpython-39/layer4/Menu.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. In file included from layer4/Menu.cpp:26: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -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-p3-i386-cpython-39/layer1/Shaker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. 1 warning generated. 4 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -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/ExecutivePython.cpp -o build/temp.freebsd-13.1-RELEASE-p3-i386-cpython-39/layer3/ExecutivePython.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer3/ExecutivePython.cpp:1: In file included from layer3/ExecutivePython.h:3: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -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-p3-i386-cpython-39/layer3/SelectorTmp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. 1 warning generated. In file included from layer3/SelectorTmp.cpp:7: In file included from layer3/Selector.h:24: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. error: command '/usr/bin/c++' failed with exit code 1 Exception ignored in: Traceback (most recent call last): File "/usr/local/lib/python3.9/multiprocessing/pool.py", line 268, in __del__ File "/usr/local/lib/python3.9/multiprocessing/queues.py", line 377, in put File "/usr/local/lib/python3.9/multiprocessing/connection.py", line 205, in send_bytes File "/usr/local/lib/python3.9/multiprocessing/connection.py", line 405, in _send_bytes AttributeError: 'NoneType' object has no attribute 'pack' *** Error code 1 Stop. make: stopped in /usr/ports/science/py-pymol