=>> Building biology/libsedml build started at Sun Mar 31 14:56:52 BST 2024 port directory: /usr/ports/biology/libsedml package name: libsedml-2.0.32 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1026 Mar 8 2023 /usr/ports/biology/libsedml/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 64e4fe193c Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 01 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/01/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/libsedml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/libsedml/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/libsedml/work/.cache HOME=/wrkdirs/usr/ports/biology/libsedml/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/libsedml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/libsedml/work/.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 CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/libsedml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/libsedml/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/libsedml/work/.cache HOME=/wrkdirs/usr/ports/biology/libsedml/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/libsedml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/libsedml/work/.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 DESTDIR=/wrkdirs/usr/ports/biology/libsedml/work/stage 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 " CCACHE_DIR="/root/.ccache" 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-- CMAKE_BUILD_TYPE="release" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/libsedml" EXAMPLESDIR="share/examples/libsedml" DATADIR="share/libsedml" WWWDIR="www/libsedml" ETCDIR="etc/libsedml" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/libsedml DOCSDIR=/usr/local/share/doc/libsedml EXAMPLESDIR=/usr/local/share/examples/libsedml WWWDIR=/usr/local/www/libsedml ETCDIR=/usr/local/etc/libsedml --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> libsedml-2.0.32 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> libsedml-2.0.32 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of libsedml-2.0.32 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by libsedml-2.0.32 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by libsedml-2.0.32 for building => SHA256 Checksum OK for fbergmann-libSEDML-v2.0.32_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by libsedml-2.0.32 for building ===> Extracting for libsedml-2.0.32 => SHA256 Checksum OK for fbergmann-libSEDML-v2.0.32_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for libsedml-2.0.32 ===> Applying FreeBSD patches for libsedml-2.0.32 from /usr/ports/biology/libsedml/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> libsedml-2.0.32 depends on package: libsbml>0 - not found ===> Installing existing package /packages/All/libsbml-5.20.2.pkg [pkg-builder.dan.net.uk] Installing libsbml-5.20.2... [pkg-builder.dan.net.uk] `-- Installing libxml2-2.11.7... [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] `-- Extracting libxml2-2.11.7: .......... done [pkg-builder.dan.net.uk] `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] | `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] Extracting libsbml-5.20.2: .......... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> libsedml-2.0.32 depends on package: libsbml>0 - found ===> Returning to build of libsedml-2.0.32 ===> libsedml-2.0.32 depends on package: libnuml>0 - not found ===> Installing existing package /packages/All/libnuml-1.1.6.pkg [pkg-builder.dan.net.uk] Installing libnuml-1.1.6... [pkg-builder.dan.net.uk] Extracting libnuml-1.1.6: .......... done ===> libsedml-2.0.32 depends on package: libnuml>0 - found ===> Returning to build of libsedml-2.0.32 ===> libsedml-2.0.32 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.28.3... [pkg-builder.dan.net.uk] `-- Installing expat-2.6.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.5... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.5: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.48.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.48.0: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.28.3: .......... done ===> libsedml-2.0.32 depends on file: /usr/local/bin/cmake - found ===> Returning to build of libsedml-2.0.32 ===> libsedml-2.0.32 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,2.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,2... [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,2: ..... done ===> libsedml-2.0.32 depends on executable: ninja - found ===> Returning to build of libsedml-2.0.32 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> libsedml-2.0.32 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for libsedml-2.0.32 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/libsedml/work/.build -- The C compiler identification is Clang 14.0.5 -- The CXX compiler identification is Clang 14.0.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /ccache/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /ccache/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working CXX compiler: /ccache/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so - found -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) -- Performing Test LIBXML_LIBXML_TEST -- Performing Test LIBXML_LIBXML_TEST - Success -- LIBXML_LIBXML_TEST = 1 -- Found BZ2: /usr/lib/libbz2.so (found version "1.0.8") -- Found ZLIB: /usr/lib/libz.so -- LIBXML_LIBXML_TEST = 1 -- Found LIBXML: /usr/local/lib/libxml2.so (found version "2.11.7") -- Found LIBSBML: sbml-static (found version "5.20.2") -- LIBXML_LIBXML_TEST = 1 -- Found LIBNUML: numl-static (found version "1.1.6") -- Looking for gzopen in /usr/lib/libz.so -- Looking for gzopen in /usr/lib/libz.so - found -- Looking for include file check.h -- Looking for include file check.h - not found -- Looking for include file expat.h -- Looking for include file expat.h - not found -- Looking for include file errno.h -- Looking for include file errno.h - found -- Looking for include file math.h -- Looking for include file math.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for include file float.h -- Looking for include file float.h - found -- Looking for sqrt in m -- Looking for sqrt in m - found -- ---------------------------------------------------------------------- libSEDML version 2.0.32 ---------------------------------------------------------------------- More information and the latest version are available online at https://github.com/fbergmann/libSEDML/ Please report problems using the issue tracker at https://github.com/fbergmann/libSEDML/issues To contact the developers directly, email fbergman@caltech.edu Configured on host 'pkg-builder.dan.net.uk' host type = FreeBSD host operating system = FreeBSD 13.2-RELEASE-p10 host CPU architecture = amd64 General build flags: CC = /ccache/libexec/ccache/cc CXX = /ccache/libexec/ccache/c++ CPPFLAGS = -DLINUX -DPACKAGE_VERSION="2.0.32" -DPACKAGE_NAME="libsedml" CFLAGS = -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC CXXFLAGS = -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC LDFLAGS = -fstack-protector-strong SBML library configuration: SBML library = /usr/local/lib/libsbml-static.a;BZ2::BZ2;ZLIB::ZLIB;LIBXML::LIBXML SBML include = -I/usr/local/include NUML library configuration: NUML library = /usr/local/lib/libnuml-static.a;sbml-static NUML include = -I/usr/local/include Other libSEDML configuration settings: Installation $prefix = /usr/local -- Value of $LD_LIBRARY_PATH = -- Using SWIG = SWIG_EXECUTABLE-NOTFOUND -- -- Using C++ namespace for libSEDML (libsedml) = no -- ---------------------------------------------------------------------- -- Configuring done (2.5s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/libsedml/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for libsedml-2.0.32 [ 0% 1/206] /ccache/libexec/ccache/c++ -DLIBSEDML_EXPORTS=1 -DLINUX -DPACKAGE_NAME=\"libsedml\" -DPACKAGE_VERSION=\"2.0.32\" -DUSE_ZLIB -Dsedml_EXPORTS -I/wrkdirs/usr/ports/biology/libsedml/work/.build/src/sedml/.. -I/wrkdirs/usr/ports/biology/libsedml/work/libSEDML-2.0.32/src/sedml/.. -I/wrkdirs/usr/ports/biology/libsedml/work/libSEDML-2.0.32/src/sedml -isystem /usr/local/include -isystem /usr/local/include/libxml2 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIC -MD -MT src/sedml/CMakeFiles/sedml.dir/common/SedOperationReturnValues.cpp.o -MF src/sedml/CMakeFiles/sedml.dir/common/SedOperationReturnValues.cpp.o.d -o src/sedml/CMakeFiles/sedml.dir/common/SedOperationReturnValues.cpp.o -c /wrkdirs/usr/ports/biology/libsedml/work/libSEDML-2.0.32/src/sedml/common/SedOperationReturnValues.cpp [ 0% 2/206] /ccache/libexec/ccache/c++ -DLIBSEDML_EXPORTS=1 -DLINUX -DPACKAGE_NAME=\"libsedml\" -DPACKAGE_VERSION=\"2.0.32\" -DUSE_ZLIB -Dsedml_EXPORTS -I/wrkdirs/usr/ports/biology/libsedml/work/.build/src/sedml/.. -I/wrkdirs/usr/ports/biology/libsedml/work/libSEDML-2.0.32/src/sedml/.. 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/usr/local/include/libxml2 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIC -MD -MT src/sedml/CMakeFiles/sedml.dir/common/libsedml-version.cpp.o -MF src/sedml/CMakeFiles/sedml.dir/common/libsedml-version.cpp.o.d -o src/sedml/CMakeFiles/sedml.dir/common/libsedml-version.cpp.o -c /wrkdirs/usr/ports/biology/libsedml/work/libSEDML-2.0.32/src/sedml/common/libsedml-version.cpp [ 1% 4/206] /ccache/libexec/ccache/c++ -DLIBSEDML_EXPORTS=1 -DLINUX -DPACKAGE_NAME=\"libsedml\" -DPACKAGE_VERSION=\"2.0.32\" -DUSE_ZLIB -Dsedml_EXPORTS -I/wrkdirs/usr/ports/biology/libsedml/work/.build/src/sedml/.. -I/wrkdirs/usr/ports/biology/libsedml/work/libSEDML-2.0.32/src/sedml/.. -I/wrkdirs/usr/ports/biology/libsedml/work/libSEDML-2.0.32/src/sedml -isystem /usr/local/include -isystem /usr/local/include/libxml2 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC -O2 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-fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -MD -MT tests/CMakeFiles/test_sedml.dir/TestRunner.cpp.o -MF tests/CMakeFiles/test_sedml.dir/TestRunner.cpp.o.d -o tests/CMakeFiles/test_sedml.dir/TestRunner.cpp.o -c /wrkdirs/usr/ports/biology/libsedml/work/libSEDML-2.0.32/tests/TestRunner.cpp [100% 206/206] : && /ccache/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fno-strict-aliasing -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fstack-protector-strong tests/CMakeFiles/test_sedml.dir/TestIssues.cpp.o tests/CMakeFiles/test_sedml.dir/TestRunner.cpp.o -o tests/test_sedml -Wl,-rpath,/usr/local/lib src/sedml/libsedml-static.a /usr/local/lib/libnuml-static.a /usr/local/lib/libsbml-static.a /usr/lib/libbz2.so /usr/local/lib/libxml2.so /usr/lib/libz.so && : =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> libsedml-2.0.32 depends on package: libsbml>0 - found ===> libsedml-2.0.32 depends on package: libnuml>0 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for libsedml-2.0.32 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/biology/libsedml/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/share/cmake/Modules/FindLIBSEDML.cmake -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/common/SedOperationReturnValues.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/common/SedmlEnumerations.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/common/common.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/common/extern.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/common/libsedml-config.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/common/sedmlfwd.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedAbstractCurve.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedAbstractTask.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedAddXML.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedAdjustableParameter.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedAlgorithm.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedAlgorithmParameter.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedAnalysis.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedAppliedDimension.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedAxis.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedBase.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedBounds.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedChange.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedChangeAttribute.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedChangeXML.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedComputeChange.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedConstructorException.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedCurve.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedDataDescription.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedDataGenerator.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedDataRange.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedDataSet.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedDataSource.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedDocument.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedElementFilter.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedError.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedErrorLog.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedErrorTable.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedExperimentReference.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedFigure.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedFill.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedFitExperiment.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedFitMapping.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedFunctionalRange.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedLeastSquareObjectiveFunction.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedLine.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOf.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfAdjustableParameters.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfAlgorithmParameters.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfAppliedDimensions.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfChanges.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfCurves.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfDataDescriptions.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfDataGenerators.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfDataSets.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfDataSources.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfExperimentReferences.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfFitExperiments.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfFitMappings.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfModels.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfOutputs.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfParameters.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfRanges.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfSetValues.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfSimulations.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfSlices.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfStyles.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfSubPlots.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfSubTasks.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfSurfaces.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfTasks.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedListOfVariables.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedMarker.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedModel.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedNamespaces.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedObjective.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedOneStep.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedOutput.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedParameter.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedParameterEstimationReport.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedParameterEstimationResultPlot.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedParameterEstimationTask.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedPlot.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedPlot2D.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedPlot3D.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedRange.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedReader.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedRemoveXML.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedRepeatedTask.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedReport.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedSetValue.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedShadedArea.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedSimulation.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedSlice.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedSteadyState.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedStyle.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedSubPlot.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedSubTask.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedSurface.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedTask.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedTypeCodes.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedTypes.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedUniformRange.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedUniformTimeCourse.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedVariable.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedVectorRange.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedVisitor.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedWaterfallPlot.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/SedWriter.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/common/libsedml-version.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/common/libsedml-config-common.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/include/sedml/common/libsedml-namespace.h -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/libsedml.so.2.0.32 -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/libsedml.so.2 -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/libsedml.so.2.0.32" to "/usr/local/lib" -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/libsedml.so -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/cmake/sedml-targets.cmake -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/cmake/sedml-targets-release.cmake -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/cmake/sedml-config.cmake -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/cmake/sedml-config-version.cmake -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/libsedml-static.a -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/cmake/sedml-static-targets.cmake -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/cmake/sedml-static-targets-release.cmake -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/cmake/sedml-static-config.cmake -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/lib/cmake/sedml-static-config-version.cmake -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/share/libsedml/LICENSE.txt -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/share/libsedml/README.md -- Installing: /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/share/libsedml/VERSION.txt /bin/rm -f -r /wrkdirs/usr/ports/biology/libsedml/work/stage/usr/local/share/cmake ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-03-31T13:56:52+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=64e4fe193c' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for libsedml-2.0.32 ===> Building libsedml-2.0.32 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for libsedml-2.0.32 build of biology/libsedml | libsedml-2.0.32 ended at Sun Mar 31 16:43:16 BST 2024 build time: 01:46:26