=>> Building science/cardioid build started at Mon May 5 10:39:21 BST 2025 port directory: /usr/ports/science/cardioid package name: cardioid-g20211026_4 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1391 Jan 27 13:48 /usr/ports/science/cardioid/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 6cce1f5b22 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 05 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE 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=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-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/14-amd64-default-dan/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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--- ===> The following configuration options are available for cardioid-g20211026_4: MFEM=off: Build with MFEM mesh library OPENMP=on: Parallel processing support via OpenMP ====> MPI (Message Passing Interface) support: you have to select exactly one of them NOMPI=off: Build without parallel processing support MPICH=on: Parallel processing support via MPICH OPENMPI=off: Parallel processing support via Open MPI ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/cardioid/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/cardioid/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/cardioid/work/.cache HOME=/wrkdirs/usr/ports/science/cardioid/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/cardioid/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/cardioid/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/science/cardioid/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/cardioid/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/cardioid/work/.cache HOME=/wrkdirs/usr/ports/science/cardioid/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/cardioid/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/cardioid/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/science/cardioid/work/stage 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 " 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-- MFEM="@comment " NO_MFEM="" MPICH="" NO_MPICH="@comment " NOMPI="@comment " NO_NOMPI="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" CMAKE_BUILD_TYPE="release" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cardioid" EXAMPLESDIR="share/examples/cardioid" DATADIR="share/cardioid" WWWDIR="www/cardioid" ETCDIR="etc/cardioid" --End PLIST_SUB-- --SUB_LIST-- MFEM="@comment " NO_MFEM="" MPICH="" NO_MPICH="@comment " NOMPI="@comment " NO_NOMPI="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cardioid DOCSDIR=/usr/local/share/doc/cardioid EXAMPLESDIR=/usr/local/share/examples/cardioid WWWDIR=/usr/local/www/cardioid ETCDIR=/usr/local/etc/cardioid --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 apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.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 pipebuf (-y) 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 ===> cardioid-g20211026_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> cardioid-g20211026_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cardioid-g20211026_4 =========================================================================== =================================================== ===== 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 cardioid-g20211026_4 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cardioid-g20211026_4 for building => SHA256 Checksum OK for LLNL-cardioid-g20211026-2f66d9f_GH0.tar.gz. => SHA256 Checksum OK for mfem-mfem-v4.4_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 cardioid-g20211026_4 for building ===> Extracting for cardioid-g20211026_4 => SHA256 Checksum OK for LLNL-cardioid-g20211026-2f66d9f_GH0.tar.gz. => SHA256 Checksum OK for mfem-mfem-v4.4_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 cardioid-g20211026_4 ===> Applying FreeBSD patches for cardioid-g20211026_4 from /usr/ports/science/cardioid/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cardioid-g20211026_4 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.6.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.31.6... [pkg-builder.dan.net.uk] `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.6_1... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.51.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.51.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.31.6: .......... done ===> cardioid-g20211026_4 depends on file: /usr/local/bin/cmake - found ===> Returning to build of cardioid-g20211026_4 ===> cardioid-g20211026_4 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,4.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,4... [pkg-builder.dan.net.uk] `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,4: ..... done ===== Message from python311-3.11.12: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> cardioid-g20211026_4 depends on executable: ninja - found ===> Returning to build of cardioid-g20211026_4 ===> cardioid-g20211026_4 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> cardioid-g20211026_4 depends on file: /usr/local/bin/ccache - found ===> Returning to build of cardioid-g20211026_4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cardioid-g20211026_4 depends on shared library: libblas.so - not found ===> Installing existing package /packages/All/blas-3.12.1.pkg [pkg-builder.dan.net.uk] Installing blas-3.12.1... [pkg-builder.dan.net.uk] `-- Installing gcc13-13.3.0_2... [pkg-builder.dan.net.uk] | `-- Installing binutils-2.44,1... [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] | `-- Extracting binutils-2.44,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | | `-- Installing mpfr-4.2.2,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] `-- Extracting gcc13-13.3.0_2: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg-builder.dan.net.uk] Extracting blas-3.12.1: ..... done ===== Message from gcc13-13.3.0_2: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> cardioid-g20211026_4 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> Returning to build of cardioid-g20211026_4 ===> cardioid-g20211026_4 depends on shared library: liblapack.so - not found ===> Installing existing package /packages/All/lapack-3.12.1.pkg [pkg-builder.dan.net.uk] Installing lapack-3.12.1... [pkg-builder.dan.net.uk] Extracting lapack-3.12.1: .......... done ===> cardioid-g20211026_4 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Returning to build of cardioid-g20211026_4 ===> cardioid-g20211026_4 depends on shared library: libmpich.so - not found ===> Installing existing package /packages/All/mpich-4.3.0.pkg [pkg-builder.dan.net.uk] Installing mpich-4.3.0... [pkg-builder.dan.net.uk] `-- Installing hwloc2-2.11.2... [pkg-builder.dan.net.uk] | `-- Installing level-zero-1.21.9... [pkg-builder.dan.net.uk] | | `-- Installing libfmt-10.2.1... [pkg-builder.dan.net.uk] | | `-- Extracting libfmt-10.2.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing spdlog-1.15.2... [pkg-builder.dan.net.uk] | | `-- Extracting spdlog-1.15.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting level-zero-1.21.9: .......... done [pkg-builder.dan.net.uk] | `-- Installing libpciaccess-0.18.1_1... [pkg-builder.dan.net.uk] | | `-- Installing hwdata-0.394,1... [pkg-builder.dan.net.uk] | | `-- Extracting hwdata-0.394,1: ...... done [pkg-builder.dan.net.uk] | `-- Extracting libpciaccess-0.18.1_1: ..... done [pkg-builder.dan.net.uk] | `-- Installing libxml2-2.11.9... [pkg-builder.dan.net.uk] | `-- Extracting libxml2-2.11.9: .......... done [pkg-builder.dan.net.uk] `-- Extracting hwloc2-2.11.2: .......... done [pkg-builder.dan.net.uk] `-- Installing json-c-0.18... [pkg-builder.dan.net.uk] `-- Extracting json-c-0.18: .......... done [pkg-builder.dan.net.uk] `-- Installing libepoll-shim-0.0.20240608... [pkg-builder.dan.net.uk] `-- Extracting libepoll-shim-0.0.20240608: .......... done [pkg-builder.dan.net.uk] `-- Installing libfabric-1.15.1_4... [pkg-builder.dan.net.uk] `-- Extracting libfabric-1.15.1_4: .......... done [pkg-builder.dan.net.uk] `-- Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_3: .......... done [pkg-builder.dan.net.uk] Extracting mpich-4.3.0: .......... done ===> cardioid-g20211026_4 depends on shared library: libmpich.so - found (/usr/local/lib/libmpich.so) ===> Returning to build of cardioid-g20211026_4 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for cardioid-g20211026_4 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/science/cardioid/work/.build CMake Warning (dev) at CMakeLists.txt:32 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is Clang 18.1.6 -- The CXX compiler identification is Clang 18.1.6 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/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: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:33 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Could NOT find Git (missing: GIT_EXECUTABLE) -- Git Support is OFF -- MPI Support is ON -- Found MPI_C: /usr/local/lib/libmpi.so (found version "4.1") -- Found MPI_CXX: /usr/local/lib/libmpicxx.so (found version "4.1") -- Found MPI: TRUE (found version "4.1") -- MPI C Compile Flags: -- MPI C Include Path: /usr/local/include/json-c;/usr/local/include/gcc13;/usr/local/include -- MPI C Link Flags: -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -- MPI C Libraries: /usr/local/lib/libmpi.so -- MPI CXX Compile Flags: -- MPI CXX Include Path: /usr/local/include -- MPI CXX Link Flags: -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -- MPI CXX Libraries: /usr/local/lib/libmpicxx.so;/usr/local/lib/libmpi.so -- MPI Executable: /usr/local/bin/mpiexec -- MPI Num Proc Flag: -n -- MPI Command Append: CMake Warning (dev) at blt/cmake/BLTMacros.cmake:314 (set): implicitly converting 'LIST' to 'STRING' type. Call Stack (most recent call first): blt/cmake/thirdparty/SetupMPI.cmake:93 (blt_register_library) blt/cmake/thirdparty/SetupThirdParty.cmake:69 (include) blt/SetupBLT.cmake:107 (include) CMakeLists.txt:48 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at blt/cmake/BLTMacros.cmake:331 (set): implicitly converting 'LIST' to 'STRING' type. Call Stack (most recent call first): blt/cmake/thirdparty/SetupMPI.cmake:93 (blt_register_library) blt/cmake/thirdparty/SetupThirdParty.cmake:69 (include) blt/SetupBLT.cmake:107 (include) CMakeLists.txt:48 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- CUDA Support is OFF -- ROCM Support is OFF -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Sphinx support is ON -- Failed to locate Sphinx executable (missing: SPHINX_EXECUTABLE) -- Valgrind support is ON -- Failed to locate Valgrind executable (missing: VALGRIND_EXECUTABLE) -- Uncrustify support is ON -- Failed to locate Uncrustify executable (missing: UNCRUSTIFY_EXECUTABLE) -- Cppcheck support is ON -- Failed to locate Cppcheck executable (missing: CPPCHECK_EXECUTABLE) CMake Warning (dev) at blt/SetupBLT.cmake:170 (set): implicitly converting 'LIST' to 'STRING' type. Call Stack (most recent call first): CMakeLists.txt:48 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at blt/SetupBLT.cmake:172 (set): implicitly converting 'LIST' to 'STRING' type. Call Stack (most recent call first): CMakeLists.txt:48 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- OpenMP Support is true -- Found OpenMP_C: -fopenmp=libomp (found version "5.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") -- Found OpenMP: TRUE (found version "5.1") -- OpenMP CXX Flags: -fopenmp=libomp -- C Compiler family is Clang -- Adding optional BLT definitions and compiler flags -- Standard C++11 selected -- Fortran support disabled. -- CMAKE_C_FLAGS flags are: -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -- CMAKE_CXX_FLAGS flags are: -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -- CMAKE_EXE_LINKER_FLAGS flags are: -fstack-protector-strong CMake Warning (dev) at blt/cmake/BLTMacros.cmake:483 (target_sources): Policy CMP0076 is not set: target_sources() command converts relative paths to absolute. Run "cmake --help-policy CMP0076" for policy details. Use the cmake_policy command to set the policy and suppress this warning. An interface source of target "simdops" has a relative path. Call Stack (most recent call first): simdops/CMakeLists.txt:2 (blt_add_library) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at blt/cmake/BLTMacros.cmake:314 (set): implicitly converting 'LIST' to 'STRING' type. Call Stack (most recent call first): CMakeLists.txt:104 (blt_register_library) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (2.0s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/science/cardioid/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for cardioid-g20211026_4 [ 0% 1/116] /usr/local/libexec/ccache/cc -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong 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/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:433:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 433 | double nActive[nTimers]; | ^~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:433:19: note: read of non-const variable 'nTimers' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:423:13: note: declared here 423 | unsigned nTimers = outputOrder.size(); | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:434:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 434 | double perfCount[nTimers][nCounters_]; | ^~~~~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:434:30: note: read of non-const variable 'nCounters_' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimersGeneric.hh:8:5: note: declared here 8 | int nCounters_=2; | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:434:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 434 | double perfCount[nTimers][nCounters_]; | ^~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:434:21: note: read of non-const variable 'nTimers' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:423:13: note: declared here 423 | unsigned nTimers = outputOrder.size(); | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:439:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 439 | long double sendBuf[bufSize]; | ^~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:439:24: note: read of non-const variable 'bufSize' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:438:13: note: declared here 438 | unsigned bufSize = 2*nTimers; | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:446:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 446 | DoubleInt minLoc[nTimers]; | ^~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:446:21: note: read of non-const variable 'nTimers' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:423:13: note: declared here 423 | unsigned nTimers = outputOrder.size(); | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:447:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 447 | DoubleInt maxLoc[nTimers]; | ^~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:447:21: note: read of non-const variable 'nTimers' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:423:13: note: declared here 423 | unsigned nTimers = outputOrder.size(); | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:448:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 448 | double sigma[nTimers]; | ^~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:448:17: note: read of non-const variable 'nTimers' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:423:13: note: declared here 423 | unsigned nTimers = outputOrder.size(); | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:470:27: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 470 | long double recvBuf[bufSize]; | ^~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:470:27: note: read of non-const variable 'bufSize' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:438:13: note: declared here 438 | unsigned bufSize = 2*nTimers; | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:489:34: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 489 | DoubleInt minLocSendBuf[nTimers]; | ^~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:489:34: note: read of non-const variable 'nTimers' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:423:13: note: declared here 423 | unsigned nTimers = outputOrder.size(); | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:490:34: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 490 | DoubleInt maxLocSendBuf[nTimers]; | ^~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:490:34: note: read of non-const variable 'nTimers' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:423:13: note: declared here 423 | unsigned nTimers = outputOrder.size(); | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:491:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 491 | double sigmaSendBuf[nTimers]; | ^~~~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:491:30: note: read of non-const variable 'nTimers' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/PerformanceTimers.cc:423:13: note: declared here 423 | unsigned nTimers = outputOrder.size(); | ^ 12 warnings generated. [ 24% 28/116] /usr/local/libexec/ccache/c++ -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIC -fopenmp=libomp -MD -MT elec/CMakeFiles/profiling.dir/unionOfStrings.cc.o -MF elec/CMakeFiles/profiling.dir/unionOfStrings.cc.o.d -o elec/CMakeFiles/profiling.dir/unionOfStrings.cc.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/unionOfStrings.cc [ 25% 29/116] : && /usr/local/bin/cmake -E rm -f lib/libprofiling.a && /usr/bin/llvm-ar qc lib/libprofiling.a elec/CMakeFiles/profiling.dir/PerformanceTimers.cc.o elec/CMakeFiles/profiling.dir/unionOfStrings.cc.o && /usr/bin/llvm-ranlib lib/libprofiling.a && : [ 25% 30/116] /usr/local/libexec/ccache/cc -DHAVE_LAPACK -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu99 -fPIC -fopenmp=libomp -MD -MT elec/CMakeFiles/ode_cpu_only.dir/TT06GatesSimd2.c.o -MF elec/CMakeFiles/ode_cpu_only.dir/TT06GatesSimd2.c.o.d -o elec/CMakeFiles/ode_cpu_only.dir/TT06GatesSimd2.c.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/TT06GatesSimd2.c In file included from /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/TT06GatesSimd2.c:3: /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/portableSIMD.h:68:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 68 | } | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/TT06GatesSimd2.c:39:7: warning: expression result unused [-Wunused-value] 39 | for (jj;jj:234:1: note: expanded from here 234 | "/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/setConductivity.cc" | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/setConductivity.cc:276:7: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 276 | abortAll(1); | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include/mpiUtils.h:39:39: note: expanded from macro 'abortAll' 39 | #define abortAll(x) abortAll_core((x),__FILE__,__LINE__) | ^ :236:1: note: expanded from here 236 | "/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/setConductivity.cc" | ^ 2 warnings generated. [ 77% 90/116] /usr/local/libexec/ccache/c++ -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simdops/include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIC -fopenmp=libomp -MD -MT elec/CMakeFiles/heart_gpu_aware.dir/assignCellsToTasks.cc.o -MF elec/CMakeFiles/heart_gpu_aware.dir/assignCellsToTasks.cc.o.d -o elec/CMakeFiles/heart_gpu_aware.dir/assignCellsToTasks.cc.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/assignCellsToTasks.cc [ 78% 91/116] /usr/local/libexec/ccache/c++ -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO 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-I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simdops/include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIC -fopenmp=libomp -MD -MT elec/CMakeFiles/heart_gpu_aware.dir/sensorFactory.cc.o -MF elec/CMakeFiles/heart_gpu_aware.dir/sensorFactory.cc.o.d -o elec/CMakeFiles/heart_gpu_aware.dir/sensorFactory.cc.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/sensorFactory.cc [ 81% 94/116] /usr/local/libexec/ccache/c++ -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simdops/include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem 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result of comparison against a string literal is unspecified (use an explicit string comparison function instead) [-Wstring-compare] 180 | if (argv[argvCursor] == "-h" || | ^ ~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/cardioid.cc:181:28: warning: result of comparison against a string literal is unspecified (use an explicit string comparison function instead) [-Wstring-compare] 181 | argv[argvCursor] == "--help") | ^ ~~~~~~~~ 2 warnings generated. [ 95% 111/116] : && /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fstack-protector-strong -fopenmp=libomp -Xlinker --dependency-file=elec/CMakeFiles/cardioid.dir/link.d elec/CMakeFiles/cardioid.dir/cardioid.cc.o -o bin/cardioid -Wl,-rpath,/usr/local/lib: lib/libheart_gpu_aware.a lib/libheart_gpu_aware.a lib/libode_gpu_aware.a lib/libheart_transport.a lib/libode_cpu_only.a lib/libprofiling.a lib/libthreading.a lib/libheart_cpu_only.a lib/libsimUtil.a /usr/local/lib/liblapack.so /usr/local/lib/libblas.so /usr/local/lib/liblapack.so /usr/local/lib/libblas.so /usr/local/lib/libmpi.so /usr/local/lib/libmpicxx.so /usr/local/lib/libmpi.so /usr/local/lib/libmpicxx.so && : [ 96% 112/116] /usr/local/libexec/ccache/c++ -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simdops/include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIE -fopenmp=libomp -MD -MT elec/CMakeFiles/singleCell.dir/singleCell.cc.o -MF elec/CMakeFiles/singleCell.dir/singleCell.cc.o.d -o elec/CMakeFiles/singleCell.dir/singleCell.cc.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/singleCell.cc /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/singleCell.cc:197:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 197 | file = object_fopen(params.object_arg[0], "r"); | ^ 1 warning generated. [ 97% 113/116] /usr/local/libexec/ccache/cc -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simdops/include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu99 -fPIE -fopenmp=libomp -MD -MT elec/CMakeFiles/singleCell.dir/singleCellOptions.c.o -MF elec/CMakeFiles/singleCell.dir/singleCellOptions.c.o.d -o elec/CMakeFiles/singleCell.dir/singleCellOptions.c.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/singleCellOptions.c [ 98% 114/116] : && /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fstack-protector-strong -fopenmp=libomp -Xlinker --dependency-file=elec/CMakeFiles/singleCell.dir/link.d elec/CMakeFiles/singleCell.dir/singleCell.cc.o elec/CMakeFiles/singleCell.dir/singleCellOptions.c.o -o bin/singleCell -Wl,-rpath,/usr/local/lib: lib/libode_gpu_aware.a lib/libheart_transport.a lib/libode_cpu_only.a lib/libprofiling.a lib/libsimUtil.a lib/libthreading.a /usr/local/lib/liblapack.so /usr/local/lib/libblas.so /usr/local/lib/liblapack.so /usr/local/lib/libblas.so /usr/local/lib/libmpi.so /usr/local/lib/libmpicxx.so /usr/local/lib/libmpi.so /usr/local/lib/libmpicxx.so && : [ 99% 115/116] /usr/local/libexec/ccache/c++ -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simdops/include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIE -fopenmp=libomp -MD -MT elec/CMakeFiles/modifyAnatomyFile.dir/modifyAnatomyFile.cc.o -MF elec/CMakeFiles/modifyAnatomyFile.dir/modifyAnatomyFile.cc.o.d -o elec/CMakeFiles/modifyAnatomyFile.dir/modifyAnatomyFile.cc.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:71:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 71 | double work[lwork]; | ^~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:71:19: note: read of non-const variable 'lwork' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:62:8: note: declared here 62 | int lwork; | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:83:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 83 | double work[lwork]; | ^~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:83:19: note: read of non-const variable 'lwork' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:62:8: note: declared here 62 | int lwork; | ^ 2 warnings generated. [100% 116/116] : && /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fstack-protector-strong -fopenmp=libomp -Xlinker --dependency-file=elec/CMakeFiles/modifyAnatomyFile.dir/link.d elec/CMakeFiles/modifyAnatomyFile.dir/modifyAnatomyFile.cc.o -o bin/modifyAnatomyFile -Wl,-rpath,/usr/local/lib lib/libheart_gpu_aware.a lib/libode_gpu_aware.a lib/libheart_transport.a lib/libode_cpu_only.a lib/libprofiling.a lib/libthreading.a lib/libheart_cpu_only.a lib/libsimUtil.a /usr/local/lib/liblapack.so /usr/local/lib/libblas.so /usr/local/lib/liblapack.so /usr/local/lib/libblas.so /usr/local/lib/libmpi.so /usr/local/lib/libmpicxx.so /usr/local/lib/libmpi.so /usr/local/lib/libmpicxx.so && : =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cardioid-g20211026_4 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.37.pkg [pkg-builder.dan.net.uk] Installing bash-5.2.37... [pkg-builder.dan.net.uk] Extracting bash-5.2.37: .......... done ===> cardioid-g20211026_4 depends on executable: bash - found ===> Returning to build of cardioid-g20211026_4 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for cardioid-g20211026_4 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/science/cardioid/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/science/cardioid/work/stage/usr/local/bin/cardioid -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/science/cardioid/work/stage/usr/local/bin/cardioid" to "/usr/local/lib" -- Installing: /wrkdirs/usr/ports/science/cardioid/work/stage/usr/local/bin/singleCell -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/science/cardioid/work/stage/usr/local/bin/singleCell" to "/usr/local/lib" -- Installing: /wrkdirs/usr/ports/science/cardioid/work/stage/usr/local/bin/compileReaction ====> 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=2025-05-05T09:39:21+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=6cce1f5b22' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for cardioid-g20211026_4 ===> Building cardioid-g20211026_4 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for cardioid-g20211026_4 build of science/cardioid | cardioid-g20211026_4 ended at Mon May 5 10:43:56 BST 2025 build time: 00:04:36