=> Building science/MOOSE-neural-simulator Started : Thursday, 19 APR 2018 at 05:12:52 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.81.g32506c-DEVELOPMENT #29: Tue Apr 10 08:49:52 PDT 2018 marino@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.0-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.0-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for MOOSE-neural-simulator-3.1.2_1: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/construction/science/MOOSE-neural-simulator XDG_CONFIG_HOME=/construction/science/MOOSE-neural-simulator HOME=/construction/science/MOOSE-neural-simulator TMPDIR="/tmp" PATH=/construction/science/MOOSE-neural-simulator/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/construction/science/MOOSE-neural-simulator XDG_CONFIG_HOME=/construction/science/MOOSE-neural-simulator HOME=/construction/science/MOOSE-neural-simulator TMPDIR="/tmp" PATH=/construction/science/MOOSE-neural-simulator/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/science/MOOSE-neural-simulator/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" PYQT_SIPDIR=share/py-sip/PyQt4 PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/MOOSE-neural-simulator" EXAMPLESDIR="share/examples/MOOSE-neural-simulator" DATADIR="share/MOOSE-neural-simulator" WWWDIR="www/MOOSE-neural-simulator" ETCDIR="etc/MOOSE-neural-simulator" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/MOOSE-neural-simulator DOCSDIR=/usr/local/share/doc/MOOSE-neural-simulator EXAMPLESDIR=/usr/local/share/examples/MOOSE-neural-simulator WWWDIR=/usr/local/www/MOOSE-neural-simulator ETCDIR=/usr/local/etc/MOOSE-neural-simulator -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.0 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500000 OSVERSION=9999999 OSREL=5.0 _OSRELEASE=5.0-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> MOOSE-neural-simulator-3.1.2_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5.txz Installing pkg-1.10.5... Extracting pkg-1.10.5: .......... done ===> MOOSE-neural-simulator-3.1.2_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by MOOSE-neural-simulator-3.1.2_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by MOOSE-neural-simulator-3.1.2_1 for building => SHA256 Checksum OK for BhallaLab-moose-3.1.2-382-gc93d23a_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by MOOSE-neural-simulator-3.1.2_1 for building ===> Extracting for MOOSE-neural-simulator-3.1.2_1 => SHA256 Checksum OK for BhallaLab-moose-3.1.2-382-gc93d23a_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for MOOSE-neural-simulator-3.1.2_1 ===> Applying ports patches for MOOSE-neural-simulator-3.1.2_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> MOOSE-neural-simulator-3.1.2_1 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-4.4.19.txz Installing bash-4.4.19... `-- Installing gettext-runtime-0.19.8.1_1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting bash-4.4.19: .......... done ===> MOOSE-neural-simulator-3.1.2_1 depends on executable: bash - found ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-numpy>0 - not found ===> Installing existing package /packages/All/py27-numpy-1.13.3_2,1.txz Installing py27-numpy-1.13.3_2,1... `-- Installing gcc5-5.5.0_2... | `-- Installing binutils-2.30_2,1... | `-- Extracting binutils-2.30_2,1: .......... done | `-- Installing gmp-6.1.2... | `-- Extracting gmp-6.1.2: .......... done | `-- Installing mpc-1.1.0... | | `-- Installing mpfr-3.1.6... | | `-- Extracting mpfr-3.1.6: .......... done | `-- Extracting mpc-1.1.0: ...... done `-- Extracting gcc5-5.5.0_2: .......... done `-- Installing openblas-0.2.20_2,1... `-- Extracting openblas-0.2.20_2,1: ......... done `-- Installing py27-setuptools-39.0.1... | `-- Installing python27-2.7.14_1... | | `-- Installing expat-2.2.5... | | `-- Extracting expat-2.2.5: .......... done | | `-- Installing libffi-3.2.1_2... | | `-- Extracting libffi-3.2.1_2: .......... done | | `-- Installing libressl-2.6.4... | | `-- Extracting libressl-2.6.4: .......... done | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting python27-2.7.14_1: .......... done `-- Extracting py27-setuptools-39.0.1: .......... done `-- Installing suitesparse-4.0.2_8... `-- Extracting suitesparse-4.0.2_8: .......... done Extracting py27-numpy-1.13.3_2,1: .......... done Message from gcc5-5.5.0_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/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unsupported by upstream. Use GCC 6 or newer instead.. Message from python27-2.7.14_1: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-numpy>0 - found ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.10.2.txz Installing cmake-3.10.2... `-- Installing curl-7.59.0... | `-- Installing ca_root_nss-3.36... | `-- Extracting ca_root_nss-3.36: ........ done | `-- Installing krb5-1.16_1... | | `-- Installing pkgconf-1.4.2,1... | | `-- Extracting pkgconf-1.4.2,1: .......... done | `-- Extracting krb5-1.16_1: .......... done | `-- Installing libnghttp2-1.31.0... | `-- Extracting libnghttp2-1.31.0: .......... done `-- Extracting curl-7.59.0: .......... done `-- Installing jsoncpp-1.8.1_3... `-- Extracting jsoncpp-1.8.1_3: .......... done `-- Installing libarchive-3.3.2,1... | `-- Installing liblz4-1.8.1.2,1... | `-- Extracting liblz4-1.8.1.2,1: .......... done | `-- Installing lzo2-2.10_1... | `-- Extracting lzo2-2.10_1: .......... done `-- Extracting libarchive-3.3.2,1: .......... done `-- Installing libuv-1.20.0... `-- Extracting libuv-1.20.0: .......... done `-- Installing rhash-1.3.5... `-- Extracting rhash-1.3.5: .......... done Extracting cmake-3.10.2: .......... done Message from ca_root_nss-3.36: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> MOOSE-neural-simulator-3.1.2_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on executable: gfortran5 - found ===> MOOSE-neural-simulator-3.1.2_1 depends on file: /usr/local/bin/python2.7 - found ===> MOOSE-neural-simulator-3.1.2_1 depends on file: /usr/local/bin/as - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> MOOSE-neural-simulator-3.1.2_1 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.4.txz Installing gsl-2.4... Extracting gsl-2.4: .......... done ===> MOOSE-neural-simulator-3.1.2_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.10.1_1.txz Installing hdf5-1.10.1_1... `-- Installing hdf-szip-2.1_2... `-- Extracting hdf-szip-2.1_2: ........ done Extracting hdf5-1.10.1_1: .......... done ===> MOOSE-neural-simulator-3.1.2_1 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on shared library: libsbml.so - not found ===> Installing existing package /packages/All/libsbml-5.16.0.txz Installing libsbml-5.16.0... `-- Installing libxml2-2.9.7... `-- Extracting libxml2-2.9.7: .......... done Extracting libsbml-5.16.0: .......... done Message from libsbml-5.16.0: ===> NOTICE: The libsbml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> MOOSE-neural-simulator-3.1.2_1 depends on shared library: libsbml.so - found (/usr/local/lib/libsbml.so) ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) ===> MOOSE-neural-simulator-3.1.2_1 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for MOOSE-neural-simulator-3.1.2_1 ===> Performing out-of-source build /bin/mkdir -p /construction/science/MOOSE-neural-simulator/.build -- The C compiler identification is GNU 5.4.1 -- The CXX compiler identification is GNU 5.4.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for git GIT_EXEC-NOTFOUND -- Building version -- Found PythonInterp: /usr/local/bin/python2.7 (found version "2.7.14") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_EXE_LINKER_FLAGS CMAKE_MODULE_LINKER_FLAGS CMAKE_NO_BUILTIN_CHRPATH CMAKE_SHARED_LINKER_FLAGS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /construction/science/MOOSE-neural-simulator/.build -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for MOOSE-neural-simulator-3.1.2_1 /usr/local/bin/cmake -H/construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a -B/construction/science/MOOSE-neural-simulator/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/science/MOOSE-neural-simulator/.build/CMakeFiles /construction/science/MOOSE-neural-simulator/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/gui.dir/all --- --- CMakeFiles/moose-core.dir/all --- --- CMakeFiles/gui.dir/all --- /usr/bin/make -f CMakeFiles/gui.dir/build.make CMakeFiles/gui.dir/depend --- CMakeFiles/moose-core.dir/all --- /usr/bin/make -f CMakeFiles/moose-core.dir/build.make CMakeFiles/moose-core.dir/depend --- CMakeFiles/gui.dir/all --- --- CMakeFiles/gui.dir/depend --- --- CMakeFiles/moose-core.dir/all --- --- CMakeFiles/moose-core.dir/depend --- --- CMakeFiles/gui.dir/all --- cd /construction/science/MOOSE-neural-simulator/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build/CMakeFiles/gui.dir/DependInfo.cmake --- CMakeFiles/moose-core.dir/all --- cd /construction/science/MOOSE-neural-simulator/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build/CMakeFiles/moose-core.dir/DependInfo.cmake --- CMakeFiles/gui.dir/all --- Scanning dependencies of target gui /usr/bin/make -f CMakeFiles/gui.dir/build.make CMakeFiles/gui.dir/build --- CMakeFiles/gui --- --- CMakeFiles/moose-core.dir/all --- Scanning dependencies of target moose-core /usr/bin/make -f CMakeFiles/moose-core.dir/build.make CMakeFiles/moose-core.dir/build --- CMakeFiles/gui.dir/all --- [ 50%] Building moose-gui --- CMakeFiles/moose-core.dir/all --- --- __moose-core_build/moose.bin --- [100%] Generating __moose-core_build/moose.bin --- CMakeFiles/gui.dir/all --- /usr/local/bin/cmake -E copy_directory /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-gui /construction/science/MOOSE-neural-simulator/.build/__moose-gui_install --- CMakeFiles/moose-core.dir/all --- MAKE=/usr/bin/make bash -c /construction/science/MOOSE-neural-simulator/.build/build_moose-core.sh + set -e + [ -z /usr/bin/make ] + echo 'Building MOOSE' Building MOOSE + export 'GSL_ROOT_DIR=' + export 'HDF5_ROOT=' + cd /construction/science/MOOSE-neural-simulator/.build/__moose-core_build + cmake '-DCMAKE_INSTALL_PREFIX=/construction/science/MOOSE-neural-simulator/.build/__moose-core_install' '-DCMAKE_BUILD_TYPE=Release' '-DWITH_BOOST=OFF' '-DPYTHON_EXECUTABLE=/usr/local/bin/python2.7' '-DMOOSE_VERSION=' /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core --- CMakeFiles/gui.dir/all --- /usr/local/bin/python2.7 -m compileall -q /construction/science/MOOSE-neural-simulator/.build/__moose-gui_install --- CMakeFiles/moose-core.dir/all --- -- The C compiler identification is GNU 5.4.1 -- The CXX compiler identification is GNU 5.4.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info --- CMakeFiles/gui.dir/all --- [100%] Built target gui --- CMakeFiles/examples.dir/all --- /usr/bin/make -f CMakeFiles/examples.dir/build.make CMakeFiles/examples.dir/depend --- CMakeFiles/examples.dir/depend --- cd /construction/science/MOOSE-neural-simulator/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build/CMakeFiles/examples.dir/DependInfo.cmake Scanning dependencies of target examples /usr/bin/make -f CMakeFiles/examples.dir/build.make CMakeFiles/examples.dir/build --- CMakeFiles/examples --- /usr/local/bin/cmake -E copy_directory /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-examples /construction/science/MOOSE-neural-simulator/.build/__moose-examples_install /usr/local/bin/python2.7 -m compileall -q /construction/science/MOOSE-neural-simulator/.build/__moose-examples_install --- CMakeFiles/moose-core.dir/all --- -- Detecting C compiler ABI info - done -- Detecting C compile features --- CMakeFiles/examples.dir/all --- [100%] Built target examples --- CMakeFiles/moose-core.dir/all --- -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test COMPILER_SUPPORTS_CXX11 -- Performing Test COMPILER_SUPPORTS_CXX11 - Success -- Performing Test COMPILER_SUPPORTS_CXX0X -- Performing Test COMPILER_SUPPORTS_CXX0X - Success -- Performing Test COMPILER_WARNS_STRICT_ALIASING -- Performing Test COMPILER_WARNS_STRICT_ALIASING - Success -- Performing Test COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN -- Performing Test COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN - Success -- Your compiler supports c++11 features. Enabling it -- Found PkgConfig: /usr/local/bin/pkg-config (found version "1.4.2") -- MOOSE Version 3.2-git -- Operating system: DragonFly -- Building for Release/No unit tests. -- GSL version : 2.4 -- Found GSL /usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so -- HDF5: Using hdf5 compiler wrapper to determine CXX configuration -- Found HDF5: /usr/local/lib/libhdf5_cpp.so;/usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so (found version "1.10.1") found components: CXX HL -- MOOSE will use following HDF5 /usr/local/lib/libhdf5_cpp.so;/usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so;/usr/local/lib/libhdf5_hl_cpp.so;/usr/local/lib/libhdf5_hl.so -- Looking for cbreak in /usr/local/lib/libncurses.so -- Looking for cbreak in /usr/local/lib/libncurses.so - found -- Found Curses: /usr/local/lib/libncurses.so -- Found Readline: /usr/local/include -- Using gsl libraries: /usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so -- Checking for module 'muparser' -- Package 'muparser', required by 'virtual:world', not found -- Using private muparser -- Shared libs: /usr/local/lib/libhdf5_cpp.so;/usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so;/usr/local/lib/libhdf5_hl_cpp.so;/usr/local/lib/libhdf5_hl.so;/usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so -- Python so extension -- Found PythonInterp: /usr/local/bin/python2.7 (found version "2.7.14") -- Found NumPy: version "1.13.3" /usr/local/lib/python2.7/site-packages/numpy/core/include -- Python include flags: -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -- Platform DragonFly-5.0-SYNTH-x86_64-64bit-ELF ======================================= If cmake did not report any error, run 'make' to build MOOSE ======================================= -- Configuring done -- Generating done -- Build files have been written to: /construction/science/MOOSE-neural-simulator/.build/__moose-core_build + /usr/bin/make Scanning dependencies of target msg [ 0%] Building CXX object msg/CMakeFiles/msg.dir/Msg.cpp.o Scanning dependencies of target muparser Scanning dependencies of target basecode [ 0%] Building CXX object external/muparser/CMakeFiles/muparser.dir/src/muParser.cpp.o Scanning dependencies of target randnum Scanning dependencies of target shell [ 1%] Building CXX object randnum/CMakeFiles/randnum.dir/Binomial.cpp.o [ 1%] Building CXX object basecode/CMakeFiles/basecode.dir/consts.cpp.o [ 1%] Building CXX object shell/CMakeFiles/shell.dir/Shell.cpp.o [ 1%] Building CXX object randnum/CMakeFiles/randnum.dir/BinomialRng.cpp.o [ 1%] Building CXX object basecode/CMakeFiles/basecode.dir/Element.cpp.o [ 1%] Building CXX object external/muparser/CMakeFiles/muparser.dir/src/muParserBase.cpp.o [ 2%] Building CXX object randnum/CMakeFiles/randnum.dir/Exponential.cpp.o [ 3%] Building CXX object msg/CMakeFiles/msg.dir/DiagonalMsg.cpp.o [ 3%] Building CXX object randnum/CMakeFiles/randnum.dir/ExponentialRng.cpp.o [ 4%] Building CXX object basecode/CMakeFiles/basecode.dir/DataElement.cpp.o [ 4%] Building CXX object msg/CMakeFiles/msg.dir/OneToAllMsg.cpp.o [ 4%] Building CXX object basecode/CMakeFiles/basecode.dir/GlobalDataElement.cpp.o [ 5%] Building CXX object shell/CMakeFiles/shell.dir/ShellCopy.cpp.o [ 6%] Building CXX object external/muparser/CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o [ 6%] Building CXX object randnum/CMakeFiles/randnum.dir/Gamma.cpp.o [ 7%] Building CXX object basecode/CMakeFiles/basecode.dir/LocalDataElement.cpp.o [ 8%] Building CXX object randnum/CMakeFiles/randnum.dir/GammaRng.cpp.o [ 8%] Building CXX object basecode/CMakeFiles/basecode.dir/Eref.cpp.o [ 8%] Building CXX object shell/CMakeFiles/shell.dir/ShellThreads.cpp.o [ 8%] Building CXX object external/muparser/CMakeFiles/muparser.dir/src/muParserCallback.cpp.o [ 9%] Building CXX object msg/CMakeFiles/msg.dir/OneToOneMsg.cpp.o [ 9%] Building CXX object basecode/CMakeFiles/basecode.dir/Finfo.cpp.o [ 9%] Building CXX object external/muparser/CMakeFiles/muparser.dir/src/muParserDLL.cpp.o [ 10%] Building CXX object external/muparser/CMakeFiles/muparser.dir/src/muParserError.cpp.o [ 10%] Building CXX object msg/CMakeFiles/msg.dir/SingleMsg.cpp.o [ 10%] Building CXX object shell/CMakeFiles/shell.dir/LoadModels.cpp.o [ 10%] Building CXX object randnum/CMakeFiles/randnum.dir/Normal.cpp.o [ 10%] Building CXX object external/muparser/CMakeFiles/muparser.dir/src/muParserInt.cpp.o /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/randnum/Normal.cpp: In static member function 'static double Normal::aliasMethod()': /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/randnum/Normal.cpp:311:50: warning: 'uniform_prime' may be used uninitialized in this function [-Wmaybe-uninitialized] v_num = (unsigned long)(d*uniform*uniform*uniform_prime); ^ [ 11%] Building CXX object randnum/CMakeFiles/randnum.dir/NormalRng.cpp.o [ 12%] Building CXX object basecode/CMakeFiles/basecode.dir/DestFinfo.cpp.o [ 13%] Building CXX object external/muparser/CMakeFiles/muparser.dir/src/muParserTest.cpp.o [ 13%] Building CXX object msg/CMakeFiles/msg.dir/SparseMsg.cpp.o [ 13%] Building CXX object basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o [ 14%] Building CXX object shell/CMakeFiles/shell.dir/SaveModels.cpp.o [ 14%] Building CXX object shell/CMakeFiles/shell.dir/Neutral.cpp.o [ 14%] Building CXX object randnum/CMakeFiles/randnum.dir/Poisson.cpp.o [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/SrcFinfo.cpp.o [ 15%] Building CXX object randnum/CMakeFiles/randnum.dir/PoissonRng.cpp.o [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/ValueFinfo.cpp.o [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/SharedFinfo.cpp.o [ 16%] Building CXX object randnum/CMakeFiles/randnum.dir/Probability.cpp.o [ 16%] Building CXX object randnum/CMakeFiles/randnum.dir/RandGenerator.cpp.o [ 16%] Building CXX object external/muparser/CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o [ 17%] Building CXX object basecode/CMakeFiles/basecode.dir/FieldElementFinfo.cpp.o [ 18%] Building CXX object msg/CMakeFiles/msg.dir/OneToOneDataIndexMsg.cpp.o [ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/FieldElement.cpp.o [ 18%] Linking CXX static library libmuparser.a [ 18%] Built target muparser [ 18%] Building CXX object msg/CMakeFiles/msg.dir/testMsg.cpp.o Scanning dependencies of target scheduling [ 18%] Building CXX object scheduling/CMakeFiles/scheduling.dir/Clock.cpp.o [ 18%] Building CXX object randnum/CMakeFiles/randnum.dir/Uniform.cpp.o [ 19%] Building CXX object randnum/CMakeFiles/randnum.dir/UniformRng.cpp.o [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/Id.cpp.o [ 19%] Building CXX object randnum/CMakeFiles/randnum.dir/mt19937ar.cpp.o [ 20%] Linking CXX static library librandnum.a [ 20%] Built target randnum Scanning dependencies of target biophysics [ 20%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IntFire.cpp.o [ 21%] Building CXX object basecode/CMakeFiles/basecode.dir/ObjId.cpp.o [ 22%] Building CXX object shell/CMakeFiles/shell.dir/Wildcard.cpp.o [ 22%] Building CXX object basecode/CMakeFiles/basecode.dir/global.cpp.o [ 23%] Linking CXX static library libmsg.a [ 23%] Built target msg Scanning dependencies of target moose_builtins [ 23%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Arith.cpp.o [ 24%] Building CXX object basecode/CMakeFiles/basecode.dir/SetGet.cpp.o [ 24%] Building CXX object shell/CMakeFiles/shell.dir/testShell.cpp.o [ 24%] Building CXX object basecode/CMakeFiles/basecode.dir/OpFuncBase.cpp.o [ 24%] Building CXX object scheduling/CMakeFiles/scheduling.dir/testScheduling.cpp.o [ 25%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Group.cpp.o [ 25%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeGen.cpp.o [ 25%] Building CXX object basecode/CMakeFiles/basecode.dir/EpFunc.cpp.o [ 26%] Building CXX object basecode/CMakeFiles/basecode.dir/HopFunc.cpp.o [ 26%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Mstring.cpp.o [ 26%] Building CXX object basecode/CMakeFiles/basecode.dir/SparseMatrix.cpp.o [ 27%] Linking CXX static library libscheduling.a [ 27%] Built target scheduling Scanning dependencies of target utility [ 28%] Building CXX object utility/CMakeFiles/utility.dir/strutil.cpp.o [ 29%] Building CXX object basecode/CMakeFiles/basecode.dir/doubleEq.cpp.o [ 29%] Building CXX object basecode/CMakeFiles/basecode.dir/testAsync.cpp.o [ 29%] Building CXX object utility/CMakeFiles/utility.dir/types.cpp.o [ 30%] Building CXX object biophysics/CMakeFiles/biophysics.dir/RandSpike.cpp.o [ 30%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Func.cpp.o [ 31%] Building CXX object utility/CMakeFiles/utility.dir/setupenv.cpp.o [ 31%] Building CXX object utility/CMakeFiles/utility.dir/numutil.cpp.o [ 31%] Linking CXX static library libshell.a [ 31%] Built target shell Scanning dependencies of target mesh [ 31%] Building CXX object mesh/CMakeFiles/mesh.dir/ChemCompt.cpp.o [ 31%] Building CXX object utility/CMakeFiles/utility.dir/Annotator.cpp.o [ 31%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CompartmentDataHolder.cpp.o [ 31%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CompartmentBase.cpp.o [ 32%] Building CXX object utility/CMakeFiles/utility.dir/Vec.cpp.o [ 32%] Building CXX object utility/CMakeFiles/utility.dir/cnpy.cpp.o [ 33%] Building CXX object mesh/CMakeFiles/mesh.dir/MeshCompt.cpp.o [ 34%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Function.cpp.o [ 34%] Linking CXX static library libbasecode.a [ 34%] Built target basecode Scanning dependencies of target moose_mpi [ 34%] Building CXX object mpi/CMakeFiles/moose_mpi.dir/PostMaster.cpp.o [ 35%] Linking CXX static library libutility.a [ 35%] Built target utility Scanning dependencies of target signeur [ 36%] Building CXX object signeur/CMakeFiles/signeur.dir/Adaptor.cpp.o [ 36%] Building CXX object mesh/CMakeFiles/mesh.dir/MeshEntry.cpp.o [ 37%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Compartment.cpp.o [ 37%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SymCompartment.cpp.o [ 37%] Building CXX object signeur/CMakeFiles/signeur.dir/testSigNeur.cpp.o [ 37%] Linking CXX static library libsigneur.a [ 37%] Built target signeur Scanning dependencies of target ksolve [ 37%] Building CXX object ksolve/CMakeFiles/ksolve.dir/KinSparseMatrix.cpp.o [ 38%] Building CXX object mpi/CMakeFiles/moose_mpi.dir/testMpi.cpp.o [ 38%] Linking CXX static library libmoose_mpi.a [ 38%] Built target moose_mpi Scanning dependencies of target hsolve [ 38%] Building CXX object hsolve/CMakeFiles/hsolve.dir/HSolveStruct.cpp.o [ 38%] Building CXX object ksolve/CMakeFiles/ksolve.dir/ZombiePool.cpp.o [ 39%] Building CXX object biophysics/CMakeFiles/biophysics.dir/GapJunction.cpp.o [ 39%] Building CXX object hsolve/CMakeFiles/hsolve.dir/HinesMatrix.cpp.o [ 40%] Building CXX object ksolve/CMakeFiles/ksolve.dir/ZombieFunction.cpp.o [ 40%] Building CXX object mesh/CMakeFiles/mesh.dir/CubeMesh.cpp.o [ 40%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Variable.cpp.o [ 40%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ChanBase.cpp.o [ 41%] Building CXX object hsolve/CMakeFiles/hsolve.dir/HSolvePassive.cpp.o [ 41%] Building CXX object ksolve/CMakeFiles/ksolve.dir/ZombieBufPool.cpp.o [ 42%] Building CXX object ksolve/CMakeFiles/ksolve.dir/ZombieReac.cpp.o [ 43%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/InputVariable.cpp.o [ 43%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ChanCommon.cpp.o [ 44%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHChannel.cpp.o [ 44%] Building CXX object ksolve/CMakeFiles/ksolve.dir/ZombieEnz.cpp.o [ 44%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/TableBase.cpp.o [ 44%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHChannelBase.cpp.o [ 44%] Building CXX object hsolve/CMakeFiles/hsolve.dir/RateLookup.cpp.o [ 44%] Building CXX object hsolve/CMakeFiles/hsolve.dir/HSolveActive.cpp.o [ 45%] Building CXX object mesh/CMakeFiles/mesh.dir/CylBase.cpp.o [ 45%] Building CXX object ksolve/CMakeFiles/ksolve.dir/ZombieMMenz.cpp.o [ 45%] Building CXX object mesh/CMakeFiles/mesh.dir/CylMesh.cpp.o [ 46%] Building CXX object ksolve/CMakeFiles/ksolve.dir/VoxelPoolsBase.cpp.o [ 47%] Building CXX object hsolve/CMakeFiles/hsolve.dir/HSolveActiveSetup.cpp.o [ 48%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHChannel2D.cpp.o [ 48%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Table.cpp.o [ 49%] Building CXX object mesh/CMakeFiles/mesh.dir/NeuroNode.cpp.o [ 49%] Building CXX object ksolve/CMakeFiles/ksolve.dir/VoxelPools.cpp.o [ 49%] Building CXX object mesh/CMakeFiles/mesh.dir/NeuroMesh.cpp.o [ 50%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Interpol.cpp.o [ 50%] Building CXX object hsolve/CMakeFiles/hsolve.dir/HSolveInterface.cpp.o [ 51%] Building CXX object ksolve/CMakeFiles/ksolve.dir/GssaVoxelPools.cpp.o [ 51%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/StimulusTable.cpp.o [ 52%] Building CXX object hsolve/CMakeFiles/hsolve.dir/HSolve.cpp.o [ 52%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHGate.cpp.o [ 52%] Building CXX object ksolve/CMakeFiles/ksolve.dir/RateTerm.cpp.o [ 53%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/TimeTable.cpp.o [ 53%] Building CXX object ksolve/CMakeFiles/ksolve.dir/FuncTerm.cpp.o [ 54%] Building CXX object ksolve/CMakeFiles/ksolve.dir/Stoich.cpp.o [ 54%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/StreamerBase.cpp.o [ 54%] Building CXX object hsolve/CMakeFiles/hsolve.dir/HSolveUtils.cpp.o /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/ksolve/Stoich.cpp: In member function 'bool Stoich::isFuncTarget(unsigned int) const': /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/ksolve/Stoich.cpp:637:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] return ( funcTarget_[poolIndex] != ~0 ); ^ [ 54%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHGate2D.cpp.o [ 54%] Building CXX object mesh/CMakeFiles/mesh.dir/SpineEntry.cpp.o [ 54%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Streamer.cpp.o [ 54%] Building CXX object hsolve/CMakeFiles/hsolve.dir/testHSolve.cpp.o [ 55%] Building CXX object hsolve/CMakeFiles/hsolve.dir/ZombieCompartment.cpp.o [ 56%] Building CXX object mesh/CMakeFiles/mesh.dir/SpineMesh.cpp.o [ 57%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CaConcBase.cpp.o [ 57%] Building CXX object hsolve/CMakeFiles/hsolve.dir/ZombieCaConc.cpp.o [ 57%] Building CXX object mesh/CMakeFiles/mesh.dir/PsdMesh.cpp.o [ 58%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Stats.cpp.o [ 58%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CaConc.cpp.o [ 59%] Building CXX object hsolve/CMakeFiles/hsolve.dir/ZombieHHChannel.cpp.o [ 59%] Building CXX object ksolve/CMakeFiles/ksolve.dir/Ksolve.cpp.o [ 60%] Building CXX object biophysics/CMakeFiles/biophysics.dir/MgBlock.cpp.o [ 60%] Linking CXX static library libhsolve.a [ 60%] Built target hsolve Scanning dependencies of target diffusion [ 60%] Building CXX object diffusion/CMakeFiles/diffusion.dir/FastMatrixElim.cpp.o [ 61%] Building CXX object mesh/CMakeFiles/mesh.dir/testMesh.cpp.o [ 61%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Interpol2D.cpp.o [ 61%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Nernst.cpp.o [ 61%] Building CXX object diffusion/CMakeFiles/diffusion.dir/DiffPoolVec.cpp.o [ 62%] Building CXX object diffusion/CMakeFiles/diffusion.dir/Dsolve.cpp.o [ 62%] Linking CXX static library libmesh.a [ 62%] Built target mesh Scanning dependencies of target device [ 62%] Building CXX object device/CMakeFiles/device.dir/PulseGen.cpp.o [ 62%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Neuron.cpp.o [ 63%] Building CXX object ksolve/CMakeFiles/ksolve.dir/Gsolve.cpp.o [ 64%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/HDF5WriterBase.cpp.o [ 64%] Building CXX object device/CMakeFiles/device.dir/DiffAmp.cpp.o [ 64%] Building CXX object diffusion/CMakeFiles/diffusion.dir/testDiffusion.cpp.o [ 65%] Building CXX object device/CMakeFiles/device.dir/PIDController.cpp.o /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/builtins/HDF5WriterBase.cpp: In function 'hid_t require_group(hid_t, std::__cxx11::string)': /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/builtins/HDF5WriterBase.cpp:87:24: warning: 'current' may be used uninitialized in this function [-Wmaybe-uninitialized] hid_t prev = file, current; ^ [ 66%] Linking CXX static library libdiffusion.a [ 66%] Built target diffusion Scanning dependencies of target benchmarks [ 67%] Building CXX object benchmarks/CMakeFiles/benchmarks.dir/benchmarks.cpp.o [ 67%] Building CXX object benchmarks/CMakeFiles/benchmarks.dir/kineticMarks.cpp.o [ 67%] Building CXX object device/CMakeFiles/device.dir/RC.cpp.o [ 67%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/NSDFWriter.cpp.o [ 68%] Linking CXX static library libbenchmarks.a [ 68%] Built target benchmarks Scanning dependencies of target kinetics [ 69%] Building CXX object kinetics/CMakeFiles/kinetics.dir/PoolBase.cpp.o [ 69%] Building CXX object ksolve/CMakeFiles/ksolve.dir/ZombiePoolInterface.cpp.o [ 70%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ReadCell.cpp.o [ 71%] Linking CXX static library libdevice.a [ 71%] Built target device Scanning dependencies of target synapse [ 72%] Building CXX object synapse/CMakeFiles/synapse.dir/GraupnerBrunel2012CaPlasticitySynHandler.cpp.o [ 72%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SwcSegment.cpp.o [ 72%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Pool.cpp.o [ 72%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ReadSwc.cpp.o [ 72%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/HDF5DataWriter.cpp.o [ 73%] Building CXX object kinetics/CMakeFiles/kinetics.dir/BufPool.cpp.o [ 74%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChan.cpp.o [ 74%] Building CXX object ksolve/CMakeFiles/ksolve.dir/testKsolve.cpp.o [ 74%] Building CXX object kinetics/CMakeFiles/kinetics.dir/ReacBase.cpp.o [ 74%] Building CXX object synapse/CMakeFiles/synapse.dir/RollingMatrix.cpp.o [ 75%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/SpikeStats.cpp.o [ 76%] Building CXX object synapse/CMakeFiles/synapse.dir/SeqSynHandler.cpp.o [ 76%] Building CXX object biophysics/CMakeFiles/biophysics.dir/NMDAChan.cpp.o [ 76%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/testBuiltins.cpp.o [ 76%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Reac.cpp.o [ 77%] Building CXX object kinetics/CMakeFiles/kinetics.dir/EnzBase.cpp.o [ 78%] Building CXX object biophysics/CMakeFiles/biophysics.dir/testBiophysics.cpp.o [ 79%] Building CXX object ksolve/CMakeFiles/ksolve.dir/SteadyStateGsl.cpp.o [ 79%] Building CXX object kinetics/CMakeFiles/kinetics.dir/CplxEnzBase.cpp.o [ 79%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IzhikevichNrn.cpp.o [ 79%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/testNSDF.cpp.o [ 80%] Linking CXX static library libmoose_builtins.a [ 80%] Built target moose_builtins Scanning dependencies of target intfire [ 80%] Building CXX object intfire/CMakeFiles/intfire.dir/AdExIF.cpp.o [ 80%] Building CXX object synapse/CMakeFiles/synapse.dir/SimpleSynHandler.cpp.o [ 81%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Enz.cpp.o [ 81%] Building CXX object kinetics/CMakeFiles/kinetics.dir/MMenz.cpp.o [ 82%] Building CXX object intfire/CMakeFiles/intfire.dir/AdThreshIF.cpp.o [ 82%] Building CXX object synapse/CMakeFiles/synapse.dir/STDPSynapse.cpp.o [ 82%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Species.cpp.o [ 83%] Building CXX object synapse/CMakeFiles/synapse.dir/STDPSynHandler.cpp.o [ 83%] Building CXX object biophysics/CMakeFiles/biophysics.dir/DifShellBase.cpp.o [ 84%] Building CXX object kinetics/CMakeFiles/kinetics.dir/ReadKkit.cpp.o [ 84%] Building CXX object intfire/CMakeFiles/intfire.dir/ExIF.cpp.o [ 84%] Linking CXX static library libksolve.a [ 84%] Built target ksolve Scanning dependencies of target copy_python_files [ 85%] Copying required python files and other files to build directory [ 85%] Built target copy_python_files [ 85%] Building CXX object synapse/CMakeFiles/synapse.dir/Synapse.cpp.o [ 86%] Building CXX object intfire/CMakeFiles/intfire.dir/IntFireBase.cpp.o [ 87%] Building CXX object biophysics/CMakeFiles/biophysics.dir/DifShell.cpp.o [ 88%] Building CXX object synapse/CMakeFiles/synapse.dir/SynHandlerBase.cpp.o [ 88%] Building CXX object biophysics/CMakeFiles/biophysics.dir/DifBufferBase.cpp.o [ 88%] Building CXX object synapse/CMakeFiles/synapse.dir/testSynapse.cpp.o [ 88%] Building CXX object intfire/CMakeFiles/intfire.dir/IzhIF.cpp.o [ 88%] Linking CXX static library libsynapse.a [ 88%] Built target synapse [ 88%] Building CXX object kinetics/CMakeFiles/kinetics.dir/WriteKkit.cpp.o [ 88%] Building CXX object intfire/CMakeFiles/intfire.dir/LIF.cpp.o [ 89%] Building CXX object intfire/CMakeFiles/intfire.dir/QIF.cpp.o [ 89%] Building CXX object intfire/CMakeFiles/intfire.dir/testIntFire.cpp.o [ 90%] Building CXX object kinetics/CMakeFiles/kinetics.dir/ReadCspace.cpp.o [ 90%] Building CXX object kinetics/CMakeFiles/kinetics.dir/lookupVolumeFromMesh.cpp.o [ 90%] Linking CXX static library libintfire.a [ 90%] Built target intfire [ 90%] Building CXX object kinetics/CMakeFiles/kinetics.dir/testKinetics.cpp.o [ 91%] Building CXX object biophysics/CMakeFiles/biophysics.dir/DifBuffer.cpp.o [ 91%] Building CXX object biophysics/CMakeFiles/biophysics.dir/MMPump.cpp.o [ 91%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Leakage.cpp.o [ 92%] Building CXX object biophysics/CMakeFiles/biophysics.dir/VectorTable.cpp.o [ 92%] Building CXX object biophysics/CMakeFiles/biophysics.dir/MarkovRateTable.cpp.o [ 93%] Building CXX object biophysics/CMakeFiles/biophysics.dir/MarkovChannel.cpp.o [ 94%] Linking CXX static library libkinetics.a [ 94%] Built target kinetics [ 94%] Building CXX object biophysics/CMakeFiles/biophysics.dir/MatrixOps.cpp.o [ 94%] Building CXX object biophysics/CMakeFiles/biophysics.dir/MarkovSolverBase.cpp.o /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/biophysics/MatrixOps.cpp: In function 'void matMatAdd(Matrix*, Matrix*, double, double, unsigned int)': /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/biophysics/MatrixOps.cpp:128:10: warning: 'C' may be used uninitialized in this function [-Wmaybe-uninitialized] Matrix *C; ^ [ 95%] Building CXX object biophysics/CMakeFiles/biophysics.dir/MarkovSolver.cpp.o [ 95%] Building CXX object biophysics/CMakeFiles/biophysics.dir/VClamp.cpp.o /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/biophysics/MarkovSolver.cpp: In member function 'Matrix* MarkovSolver::computePadeApproximant(Matrix*, unsigned int)': /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/biophysics/MarkovSolver.cpp:221:9: warning: 'V' may be used uninitialized in this function [-Wmaybe-uninitialized] delete V; ^ /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core/biophysics/MarkovSolver.cpp:88:10: warning: 'padeCoeffs' may be used uninitialized in this function [-Wmaybe-uninitialized] double *padeCoeffs; ^ [ 95%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Spine.cpp.o [ 96%] Building CXX object biophysics/CMakeFiles/biophysics.dir/MarkovGslSolver.cpp.o [ 96%] Linking CXX static library libbiophysics.a [ 96%] Built target biophysics Scanning dependencies of target libmoose Scanning dependencies of target _moose [ 96%] Building CXX object CMakeFiles/libmoose.dir/basecode/main.cpp.o [ 97%] Building CXX object pymoose/CMakeFiles/_moose.dir/moosemodule.cpp.o [ 97%] Building CXX object pymoose/CMakeFiles/_moose.dir/mfield.cpp.o [ 97%] Building CXX object pymoose/CMakeFiles/_moose.dir/vec.cpp.o [ 97%] Building CXX object pymoose/CMakeFiles/_moose.dir/pymooseinit.cpp.o [ 98%] Linking CXX shared library libmoose.so [ 98%] Building CXX object pymoose/CMakeFiles/_moose.dir/melement.cpp.o builtins/libmoose_builtins.a(testNSDF.cpp.o): In function `testCreateStringDataset()': testNSDF.cpp:(.text+0x4e): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() [ 98%] Built target libmoose [ 99%] Building CXX object pymoose/CMakeFiles/_moose.dir/test_moosemodule.cpp.o [ 99%] Building CXX object pymoose/CMakeFiles/_moose.dir/PyRun.cpp.o [100%] Linking CXX shared module ../python/moose/_moose.so ../builtins/libmoose_builtins.a(testNSDF.cpp.o): In function `testCreateStringDataset()': testNSDF.cpp:(.text+0x4e): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() MOOSE python extention is successfully built. Now 1. Run 'make install' to install it single user. 2. Run 'sudo make install' to install it system-wide. After installation, 'pip uninstall moose' will uninstall moose. [100%] Built target _moose + ctest -output-on-failure Test project /construction/science/MOOSE-neural-simulator/.build/__moose-core_build Start 1: test_accessing_existing_paths 1/24 Test #1: test_accessing_existing_paths .... Passed 0.62 sec Start 2: test_connectionLists 2/24 Test #2: test_connectionLists ............. Passed 0.67 sec Start 3: test_difshells 3/24 Test #3: test_difshells ...................***Failed 0.27 sec Start 4: test_docs 4/24 Test #4: test_docs ........................ Passed 0.35 sec Start 5: test_function 5/24 Test #5: test_function .................... Passed 0.39 sec Start 6: test_hsolve_externalCalcium 6/24 Test #6: test_hsolve_externalCalcium ......***Failed 0.33 sec Start 7: test_import 7/24 Test #7: test_import ......................***Failed 0.44 sec Start 8: test_kkit 8/24 Test #8: test_kkit ........................***Failed 0.02 sec Start 9: test_ksolve 9/24 Test #9: test_ksolve ...................... Passed 0.73 sec Start 10: test_moose_paths 10/24 Test #10: test_moose_paths ................. Passed 0.44 sec Start 11: test_muparser 11/24 Test #11: test_muparser ....................***Failed 0.29 sec Start 12: test_neuroml 12/24 Test #12: test_neuroml .....................***Failed 0.34 sec Start 13: test_nsdf 13/24 Test #13: test_nsdf ........................ Passed 1.22 sec Start 14: test_paths 14/24 Test #14: test_paths ....................... Passed 0.45 sec Start 15: test_pymoose 15/24 Test #15: test_pymoose ..................... Passed 0.42 sec Start 16: test_pyrun 16/24 Test #16: test_pyrun ....................... Passed 0.30 sec Start 17: test_rdesigneur 17/24 Test #17: test_rdesigneur ..................***Failed 0.36 sec Start 18: test_sbml 18/24 Test #18: test_sbml ........................***Failed 0.70 sec Start 19: test_snippets 19/24 Test #19: test_snippets .................... Passed 0.04 sec Start 20: test_streamer 20/24 Test #20: test_streamer .................... Passed 0.61 sec Start 21: test_synchan 21/24 Test #21: test_synchan ..................... Passed 0.33 sec Start 22: test_table_streaming_support 22/24 Test #22: test_table_streaming_support ..... Passed 0.42 sec Start 23: test_utils 23/24 Test #23: test_utils .......................***Failed 0.25 sec Start 24: test_vec 24/24 Test #24: test_vec ......................... Passed 0.27 sec 63% tests passed, 9 tests failed out of 24 Total Test time (real) = 10.27 sec The following tests FAILED: 3 - test_difshells (Failed) 6 - test_hsolve_externalCalcium (Failed) 7 - test_import (Failed) 8 - test_kkit (Failed) 11 - test_muparser (Failed) 12 - test_neuroml (Failed) 17 - test_rdesigneur (Failed) 18 - test_sbml (Failed) 23 - test_utils (Failed) Errors while running CTest + echo 'Some tests failed' Some tests failed + /usr/bin/make install [ 4%] Built target msg [ 7%] Built target muparser [ 16%] Built target basecode [ 23%] Built target randnum [ 24%] Built target scheduling [ 33%] Built target moose_builtins [ 49%] Built target biophysics [ 55%] Built target moose_mpi [ 54%] Built target mesh [ 56%] Built target signeur [ 61%] Built target hsolve [ 68%] Built target ksolve [ 70%] Built target diffusion [ 74%] Built target utility [ 76%] Built target device [ 78%] Built target benchmarks [ 79%] Copying required python files and other files to build directory [ 86%] Built target kinetics [ 89%] Built target intfire [ 93%] Built target synapse [ 93%] Built target copy_python_files [ 96%] Built target shell [100%] Built target libmoose [100%] Built target _moose Install the project... -- Install configuration: "Release" Failed to read VERSION [Errno 2] No such file or directory: '/construction/science/MOOSE-neural-simulator/.build/__moose-core_build/python/../VERSION' Using default 3.2.git [WARN] Failed to determine importlib suffix running install running build running build_py creating build creating build/lib creating build/lib/rdesigneur copying rdesigneur/rmoogli.py -> build/lib/rdesigneur copying rdesigneur/rdesigneurProtos.py -> build/lib/rdesigneur copying rdesigneur/__init__.py -> build/lib/rdesigneur copying rdesigneur/rdesigneur.py -> build/lib/rdesigneur creating build/lib/moose copying moose/constants.py -> build/lib/moose copying moose/OrderedDict.py -> build/lib/moose copying moose/methods_utils.py -> build/lib/moose copying moose/alternate.py -> build/lib/moose copying moose/print_utils.py -> build/lib/moose copying moose/hdfutil.py -> build/lib/moose copying moose/utils.py -> build/lib/moose copying moose/optimizer_interface.py -> build/lib/moose copying moose/moose_test.py -> build/lib/moose copying moose/graph_utils.py -> build/lib/moose copying moose/moose_constants.py -> build/lib/moose copying moose/recording.py -> build/lib/moose copying moose/graphutil.py -> build/lib/moose copying moose/plot_utils.py -> build/lib/moose copying moose/moose.py -> build/lib/moose copying moose/__init__.py -> build/lib/moose copying moose/moose_config.py -> build/lib/moose creating build/lib/moose/SBML copying moose/SBML/readSBML.py -> build/lib/moose/SBML copying moose/SBML/__init__.py -> build/lib/moose/SBML copying moose/SBML/writeSBML.py -> build/lib/moose/SBML copying moose/SBML/validation.py -> build/lib/moose/SBML creating build/lib/moose/neuroml copying moose/neuroml/ChannelML.py -> build/lib/moose/neuroml copying moose/neuroml/__init__.py -> build/lib/moose/neuroml copying moose/neuroml/MorphML.py -> build/lib/moose/neuroml copying moose/neuroml/NeuroML.py -> build/lib/moose/neuroml copying moose/neuroml/NetworkML.py -> build/lib/moose/neuroml copying moose/neuroml/utils.py -> build/lib/moose/neuroml creating build/lib/moose/genesis copying moose/genesis/__init__.py -> build/lib/moose/genesis copying moose/genesis/writeKkit.py -> build/lib/moose/genesis creating build/lib/moose/chemUtil copying moose/chemUtil/graphUtils.py -> build/lib/moose/chemUtil copying moose/chemUtil/add_Delete_ChemicalSolver.py -> build/lib/moose/chemUtil copying moose/chemUtil/chemConnectUtil.py -> build/lib/moose/chemUtil copying moose/chemUtil/__init__.py -> build/lib/moose/chemUtil creating build/lib/moose/chemMerge copying moose/chemMerge/merge.py -> build/lib/moose/chemMerge copying moose/chemMerge/__init__.py -> build/lib/moose/chemMerge copying moose/chemMerge/mtypes.py -> build/lib/moose/chemMerge copying moose/_moose.so -> build/lib/moose running install_lib creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7 creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/_moose.so -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge copying build/lib/moose/chemMerge/mtypes.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge copying build/lib/moose/chemMerge/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge copying build/lib/moose/chemMerge/merge.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil copying build/lib/moose/chemUtil/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil copying build/lib/moose/chemUtil/chemConnectUtil.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil copying build/lib/moose/chemUtil/add_Delete_ChemicalSolver.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil copying build/lib/moose/chemUtil/graphUtils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/genesis copying build/lib/moose/genesis/writeKkit.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/genesis copying build/lib/moose/genesis/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/genesis creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/NetworkML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/NeuroML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/MorphML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/ChannelML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML copying build/lib/moose/SBML/validation.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML copying build/lib/moose/SBML/writeSBML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML copying build/lib/moose/SBML/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML copying build/lib/moose/SBML/readSBML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML copying build/lib/moose/moose_config.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/moose.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/plot_utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/graphutil.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/recording.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/moose_constants.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/graph_utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/moose_test.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/optimizer_interface.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/hdfutil.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/print_utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/alternate.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/methods_utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/OrderedDict.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/constants.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose creating /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur copying build/lib/rdesigneur/rdesigneur.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur copying build/lib/rdesigneur/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur copying build/lib/rdesigneur/rdesigneurProtos.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur copying build/lib/rdesigneur/rmoogli.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge/mtypes.py to mtypes.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge/merge.py to merge.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil/chemConnectUtil.py to chemConnectUtil.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil/add_Delete_ChemicalSolver.py to add_Delete_ChemicalSolver.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil/graphUtils.py to graphUtils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/genesis/writeKkit.py to writeKkit.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/genesis/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/utils.py to utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/NetworkML.py to NetworkML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/NeuroML.py to NeuroML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/MorphML.py to MorphML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/ChannelML.py to ChannelML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML/validation.py to validation.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML/writeSBML.py to writeSBML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML/readSBML.py to readSBML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/moose_config.py to moose_config.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/moose.py to moose.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/plot_utils.py to plot_utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/graphutil.py to graphutil.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/recording.py to recording.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/moose_constants.py to moose_constants.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/graph_utils.py to graph_utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/moose_test.py to moose_test.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/optimizer_interface.py to optimizer_interface.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/utils.py to utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/hdfutil.py to hdfutil.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/print_utils.py to print_utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/alternate.py to alternate.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/methods_utils.py to methods_utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/OrderedDict.py to OrderedDict.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/constants.py to constants.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur/rdesigneur.py to rdesigneur.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur/rdesigneurProtos.py to rdesigneurProtos.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur/rmoogli.py to rmoogli.pyc running install_egg_info Writing /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose-3.2.git-py2.7.egg-info [100%] Built target moose-core --- CMakeFiles/moose.dir/all --- /usr/bin/make -f CMakeFiles/moose.dir/build.make CMakeFiles/moose.dir/depend --- CMakeFiles/moose.dir/depend --- cd /construction/science/MOOSE-neural-simulator/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build/CMakeFiles/moose.dir/DependInfo.cmake Scanning dependencies of target moose /usr/bin/make -f CMakeFiles/moose.dir/build.make CMakeFiles/moose.dir/build [100%] Built target moose /usr/local/bin/cmake -E cmake_progress_start /construction/science/MOOSE-neural-simulator/.build/CMakeFiles 0 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-numpy>0 - found ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-matplotlib>=1.1.0 - not found ===> Installing existing package /packages/All/py27-matplotlib-2.1.2_2.txz Installing py27-matplotlib-2.1.2_2... `-- Installing atk-2.24.0... | `-- Installing glib-2.50.3_1,1... | | `-- Installing libiconv-1.14_11... | | `-- Extracting libiconv-1.14_11: .......... done | | `-- Installing pcre-8.40_1... | | `-- Extracting pcre-8.40_1: .......... done | | `-- Installing perl5-5.26.1... | | `-- Extracting perl5-5.26.1: .......... done | `-- Extracting glib-2.50.3_1,1: .......... done No schema files found: doing nothing. `-- Extracting atk-2.24.0: .......... done `-- Installing cairo-1.14.8_1,2... | `-- Installing dri2proto-2.8... | `-- Extracting dri2proto-2.8: .... done | `-- Installing fontconfig-2.12.1_3,1... | | `-- Installing freetype2-2.9_1... | | `-- Extracting freetype2-2.9_1: .......... done | `-- Extracting fontconfig-2.12.1_3,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded | `-- Installing glproto-1.4.17... | `-- Extracting glproto-1.4.17: ...... done | `-- Installing libX11-1.6.5,1... | | `-- Installing kbproto-1.0.7... | | `-- Extracting kbproto-1.0.7: .......... done | | `-- Installing libXau-1.0.8_3... | | `-- Installing xproto-7.0.31... | | `-- Extracting xproto-7.0.31: .......... done | | `-- Extracting libXau-1.0.8_3: .......... done | | `-- Installing libXdmcp-1.1.2... | | `-- Extracting libXdmcp-1.1.2: ......... done | | `-- Installing libxcb-1.12_2... | | `-- Installing libpthread-stubs-0.4... | | `-- Extracting libpthread-stubs-0.4: .... done | | `-- Extracting libxcb-1.12_2: .......... done | `-- Extracting libX11-1.6.5,1: .......... done | `-- Installing libXext-1.3.3_1,1... | | `-- Installing xextproto-7.3.0... | | `-- Extracting xextproto-7.3.0: .......... done | `-- Extracting libXext-1.3.3_1,1: .......... done | `-- Installing libXrender-0.9.10... | | `-- Installing renderproto-0.11.1... | | `-- Extracting renderproto-0.11.1: .... done | `-- Extracting libXrender-0.9.10: .......... done | `-- Installing mesa-libs-17.3.1... | | `-- Installing libXdamage-1.1.4_3... | | `-- Installing damageproto-1.2.1... | | `-- Extracting damageproto-1.2.1: .... done | | `-- Installing libXfixes-5.0.3... | | | `-- Installing fixesproto-5.0... | | | `-- Extracting fixesproto-5.0: .... done | | `-- Extracting libXfixes-5.0.3: .......... done | | `-- Extracting libXdamage-1.1.4_3: ...... done | | `-- Installing libXxf86vm-1.1.4_1... | | `-- Installing xf86vidmodeproto-2.3.1... | | `-- Extracting xf86vidmodeproto-2.3.1: .... done | | `-- Extracting libXxf86vm-1.1.4_1: .......... done | | `-- Installing libdrm-2.4.89,1... | | `-- Installing libpciaccess-0.13.5... | | | `-- Installing pciids-20180219... | | | `-- Extracting pciids-20180219: ..... done | | `-- Extracting libpciaccess-0.13.5: ...... done | | `-- Extracting libdrm-2.4.89,1: .......... done | | `-- Installing libelf-0.8.13_3... | | `-- Extracting libelf-0.8.13_3: .......... done | | `-- Installing libxshmfence-1.2_2... | | `-- Extracting libxshmfence-1.2_2: ......... done | `-- Extracting mesa-libs-17.3.1: .......... done | `-- Installing pixman-0.34.0... | `-- Extracting pixman-0.34.0: .......... done | `-- Installing png-1.6.34... | `-- Extracting png-1.6.34: .......... done | `-- Installing xcb-util-renderutil-0.3.9_1... | | `-- Installing xcb-util-0.4.0_2,1... | | `-- Extracting xcb-util-0.4.0_2,1: .......... done | `-- Extracting xcb-util-renderutil-0.3.9_1: ...... done `-- Extracting cairo-1.14.8_1,2: .......... done `-- Installing gdk-pixbuf2-2.36.11... | `-- Installing jasper-1.900.1_17... | | `-- Installing jpeg-turbo-1.5.3... | | `-- Extracting jpeg-turbo-1.5.3: .......... done | `-- Extracting jasper-1.900.1_17: .......... done | `-- Installing libXi-1.7.9,1... | | `-- Installing inputproto-2.3.2... | | `-- Extracting inputproto-2.3.2: ........ done | `-- Extracting libXi-1.7.9,1: .......... done | `-- Installing libXt-1.1.5,1... | | `-- Installing libSM-1.2.2_3,1... | | `-- Installing libICE-1.0.9_1,1... | | `-- Extracting libICE-1.0.9_1,1: .......... done | | `-- Extracting libSM-1.2.2_3,1: .......... done | `-- Extracting libXt-1.1.5,1: .......... done | `-- Installing shared-mime-info-1.8... | `-- Extracting shared-mime-info-1.8: .......... done | `-- Installing tiff-4.0.9_1... | | `-- Installing jbigkit-2.1_1... | | `-- Extracting jbigkit-2.1_1: .......... done | `-- Extracting tiff-4.0.9_1: .......... done `-- Extracting gdk-pixbuf2-2.36.11: .......... done `-- Installing gtk2-2.24.32... | `-- Installing cups-2.2.6... | | `-- Installing avahi-app-0.6.31_6... | | `-- Installing dbus-glib-0.108... | | | `-- Installing dbus-1.10.16_1... ===> Creating 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Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. | | | `-- Extracting dbus-1.10.16_1: ......... done | | `-- Extracting dbus-glib-0.108: .......... done | | `-- Installing gdbm-1.13_1... | | `-- Extracting gdbm-1.13_1: .......... done | | `-- Installing gnome_subr-1.0... | | `-- Extracting gnome_subr-1.0: .... done | | `-- Installing gobject-introspection-1.50.0_1,1... | | `-- Extracting gobject-introspection-1.50.0_1,1: .......... done | | `-- Installing libdaemon-0.14_1... | | `-- Extracting libdaemon-0.14_1: .......... done ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. | | `-- Extracting avahi-app-0.6.31_6: .......... done | | `-- Installing gnutls-3.5.18... | | `-- Installing libidn2-2.0.4... | | | `-- Installing libunistring-0.9.9... | | | `-- Extracting libunistring-0.9.9: .......... done | | `-- Extracting libidn2-2.0.4: .......... done | | `-- Installing libtasn1-4.13... | | `-- Extracting libtasn1-4.13: .......... done | | `-- Installing nettle-3.4... | | `-- Extracting nettle-3.4: .......... done | | `-- Installing p11-kit-0.23.10... | | `-- Extracting p11-kit-0.23.10: .......... done | | `-- Installing trousers-0.3.14_2... | | | `-- Installing tpm-emulator-0.7.4_2... ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | | `-- Extracting tpm-emulator-0.7.4_2: ......... done ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | `-- Extracting trousers-0.3.14_2: .......... done | | `-- Extracting gnutls-3.5.18: .......... done | | `-- Installing libpaper-1.1.24.4... | | `-- Extracting libpaper-1.1.24.4: .......... done ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. | `-- Extracting cups-2.2.6: .......... done | `-- Installing gtk-update-icon-cache-2.24.32... | | `-- Installing hicolor-icon-theme-0.15... | | `-- Extracting hicolor-icon-theme-0.15: . done | | `-- Installing libXcomposite-0.4.4_3,1... | | `-- Installing compositeproto-0.4.2... | | `-- Extracting compositeproto-0.4.2: ....... done | | `-- Extracting libXcomposite-0.4.4_3,1: .......... done | | `-- Installing libXcursor-1.1.15... | | `-- Extracting libXcursor-1.1.15: .......... done | | `-- Installing libXinerama-1.1.3_3,1... | | `-- Installing xineramaproto-1.2.1... | | `-- Extracting xineramaproto-1.2.1: .. done | | `-- Extracting libXinerama-1.1.3_3,1: .......... done | | `-- Installing libXrandr-1.5.1... | | `-- Installing randrproto-1.5.0... | | `-- Extracting randrproto-1.5.0: ....... done | | `-- Extracting libXrandr-1.5.1: .......... done | | `-- Installing pango-1.42.0... | | `-- Installing encodings-1.0.4_4,1... | | | `-- Installing font-util-1.3.1... | | | `-- Extracting font-util-1.3.1: .......... done | | `-- Extracting encodings-1.0.4_4,1: .......... done | | `-- Installing fribidi-0.19.7... | | `-- Extracting fribidi-0.19.7: .......... done | | `-- Installing harfbuzz-1.7.6... | | | `-- Installing graphite2-1.3.11... | | | `-- Extracting graphite2-1.3.11: .......... done | | `-- Extracting harfbuzz-1.7.6: .......... done | | `-- Installing libXft-2.3.2_1... | | `-- Extracting libXft-2.3.2_1: .......... done | | `-- Installing xorg-fonts-truetype-7.7_1... | | | `-- Installing dejavu-2.37... | | | `-- Installing mkfontdir-1.0.7... | | | | `-- Installing mkfontscale-1.1.2... | | | | `-- Installing libfontenc-1.1.3_1... | | | | `-- Extracting libfontenc-1.1.3_1: ......... done | | | | `-- Extracting mkfontscale-1.1.2: .. done | | | `-- Extracting mkfontdir-1.0.7: .. done | | | `-- Extracting dejavu-2.37: .......... done | | | `-- Installing font-bh-ttf-1.0.3_3... | | | `-- Extracting font-bh-ttf-1.0.3_3: .......... done | | | `-- Installing font-misc-ethiopic-1.0.3_3... | | | `-- Extracting font-misc-ethiopic-1.0.3_3: ... done | | | `-- Installing font-misc-meltho-1.0.3_3... | | | `-- Extracting font-misc-meltho-1.0.3_3: .......... done | | `-- Extracting pango-1.42.0: .......... done | `-- Extracting gtk-update-icon-cache-2.24.32: .... done `-- Extracting gtk2-2.24.32: .......... done `-- Installing libglade2-2.6.4_9... | `-- Installing xmlcatmgr-2.2_2... | `-- Extracting xmlcatmgr-2.2_2: ......... done + Creating /usr/local/share/sgml/catalog + Registering CATALOG catalog.ports (SGML) + Creating /usr/local/share/sgml/catalog.ports + Creating /usr/local/share/xml/catalog + Registering nextCatalog catalog.ports (XML) + Creating /usr/local/share/xml/catalog.ports `-- Extracting libglade2-2.6.4_9: .......... done `-- Installing py27-backports.functools_lru_cache-1.5... | `-- Installing py27-backports-1... | `-- Extracting py27-backports-1: ...... done `-- Extracting py27-backports.functools_lru_cache-1.5: .......... done `-- Installing py27-cycler-0.10.0... | `-- Installing py27-six-1.11.0... | `-- Extracting py27-six-1.11.0: .......... done `-- Extracting py27-cycler-0.10.0: .......... done `-- Installing py27-dateutil-2.6.1... `-- Extracting py27-dateutil-2.6.1: .......... done `-- Installing py27-gobject-2.28.6_8... | `-- Installing py27-cairo-1.14.1... | `-- Extracting py27-cairo-1.14.1: .......... done `-- Extracting py27-gobject-2.28.6_8: .......... done `-- Installing py27-gtk2-2.24.0_5... `-- Extracting py27-gtk2-2.24.0_5: .......... done `-- Installing py27-pyparsing-2.2.0... `-- Extracting py27-pyparsing-2.2.0: .......... done `-- Installing py27-pytz-2018.3,1... `-- Extracting py27-pytz-2018.3,1: .......... done `-- Installing py27-tkinter-2.7.14_6... | `-- Installing tcl86-8.6.8... | `-- Extracting tcl86-8.6.8: .......... done | `-- Installing tk86-8.6.8_2... | | `-- Installing libXScrnSaver-1.2.2_3... | | `-- Installing scrnsaverproto-1.2.2... | | `-- Extracting scrnsaverproto-1.2.2: ... done | | `-- Extracting libXScrnSaver-1.2.2_3: .......... done | `-- Extracting tk86-8.6.8_2: .......... done `-- Extracting py27-tkinter-2.7.14_6: ........ done `-- Installing py27-tornado-5.0... | `-- Installing py27-backports_abc-0.5... | `-- Extracting py27-backports_abc-0.5: .......... done | `-- Installing py27-singledispatch-3.4.0.3_1... | `-- Extracting py27-singledispatch-3.4.0.3_1: .......... done `-- Extracting py27-tornado-5.0: .......... done Extracting py27-matplotlib-2.1.2_2: .......... done Message from perl5-5.26.1: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Message from freetype2-2.9_1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). Message from trousers-0.3.14_2: To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Message from dejavu-2.37: Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Message from xmlcatmgr-2.2_2: The following catalogs are installed: 1) /usr/local/share/sgml/catalog The top level catalog for SGML stuff. It is not changed by any ports/packages except textproc/xmlcatmgr. 2) /usr/local/share/sgml/catalog.ports This catalog is for handling SGML stuff installed under /usr/local/share/sgml. It is changed by ports/packages. 3) /usr/local/share/xml/catalog The top level catalog for XML stuff. It is not changed by any ports/packages except textproc/xmlcatmgr. 4) /usr/local/share/xml/catalog.ports This catalog is for handling XML stuff installed under /usr/local/share/xml. It is changed by ports/packages. ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-matplotlib>=1.1.0 - found ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-networkx>=1.0 - not found ===> Installing existing package /packages/All/py27-networkx-1.10_4.txz Installing py27-networkx-1.10_4... `-- Installing py27-decorator-4.2.1... `-- Extracting py27-decorator-4.2.1: .......... done `-- Installing py27-pygraphviz-1.3.1... | `-- Installing graphviz-2.40.1_4... | | `-- Installing libXaw-1.0.13,2... | | `-- Installing libXmu-1.1.2_3,1... | | `-- Extracting libXmu-1.1.2_3,1: .......... done | | `-- Installing libXp-1.0.3,1... | | | `-- Installing printproto-1.0.5... | | | `-- Extracting printproto-1.0.5: .... done | | `-- Extracting libXp-1.0.3,1: .......... done | | `-- Installing libXpm-3.5.12... | | `-- Extracting libXpm-3.5.12: .......... done | | `-- Extracting libXaw-1.0.13,2: .......... done | | `-- Installing libgd-2.2.4_1,1... | | `-- Installing webp-0.6.1... | | | `-- Installing giflib-5.1.4... | | | `-- Extracting giflib-5.1.4: .......... done | | `-- Extracting webp-0.6.1: .......... done | | `-- Extracting libgd-2.2.4_1,1: .......... done | | `-- Installing libltdl-2.4.6... | | `-- Extracting libltdl-2.4.6: .......... done | `-- Extracting graphviz-2.40.1_4: .......... done `-- Extracting py27-pygraphviz-1.3.1: .......... done `-- Installing py27-scikit-sparse-0.2_5... | `-- Installing py27-scipy-0.19.0_5... | `-- Extracting py27-scipy-0.19.0_5: .......... done `-- Extracting py27-scikit-sparse-0.2_5: .......... done `-- Installing py27-yaml-3.12... `-- Extracting py27-yaml-3.12: .......... done Extracting py27-networkx-1.10_4: .......... done ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-networkx>=1.0 - found ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-pygraphviz>=0 - found ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-suds-jurko>=0.4 - not found ===> Installing existing package /packages/All/py27-suds-jurko-0.6.txz Installing py27-suds-jurko-0.6... Extracting py27-suds-jurko-0.6: .......... done ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-suds-jurko>=0.4 - found ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on executable: gfortran5 - found ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-qt4-core>=4.12.1 - not found ===> Installing existing package /packages/All/py27-qt4-core-4.12.1_6,1.txz Installing py27-qt4-core-4.12.1_6,1... `-- Installing py27-sip-4.19.8,1... `-- Extracting py27-sip-4.19.8,1: .......... done `-- Installing qscintilla2-2.10.3,1... | `-- Installing qt4-corelib-4.8.7_11... | | `-- Installing icu-60.2_2,1... | | `-- Extracting icu-60.2_2,1: .......... done | | `-- Installing qtchooser-39... | | `-- Extracting qtchooser-39: .......... done | `-- Extracting qt4-corelib-4.8.7_11: .......... done | `-- Installing qt4-designer-4.8.7_1... | | `-- Installing qt4-assistant-4.8.7_1... | | `-- Installing qt4-doc-4.8.7_1... | | `-- Extracting qt4-doc-4.8.7_1: .......... done | | `-- Installing qt4-gui-4.8.7_3... | | | `-- Installing xdg-utils-1.1.1... | | | `-- Installing xprop-1.2.2... | | | `-- Extracting xprop-1.2.2: .. done | | | `-- Installing xset-1.2.3_1... | | | | `-- Installing libXfontcache-1.0.5_3... | | | | `-- Installing fontcacheproto-0.1.3... | | | | `-- Extracting fontcacheproto-0.1.3: .... done | | | | `-- Extracting libXfontcache-1.0.5_3: .......... done | | | `-- Extracting xset-1.2.3_1: .. done | | | `-- Extracting xdg-utils-1.1.1: .......... done | | `-- Extracting qt4-gui-4.8.7_3: .......... done | | `-- Installing qt4-help-4.8.7_2... | | | `-- Installing qt4-clucene-4.8.7_2... | | | `-- Extracting qt4-clucene-4.8.7_2: .......... done | | | `-- Installing qt4-network-4.8.7_3... | | | `-- Extracting qt4-network-4.8.7_3: .......... done | | | `-- Installing qt4-sql-4.8.7_2... | | | `-- Extracting qt4-sql-4.8.7_2: .......... done | | | `-- Installing qt4-sqlite-plugin-4.8.7_4... | | | `-- Installing sqlite3-3.22.0_1... | | | `-- Extracting sqlite3-3.22.0_1: .......... done | | | `-- Extracting qt4-sqlite-plugin-4.8.7_4: .... done | | | `-- Installing qt4-xml-4.8.7_2... | | | `-- Extracting qt4-xml-4.8.7_2: .......... done | | `-- Extracting qt4-help-4.8.7_2: .......... done | | `-- Installing qt4-webkit-4.8.7_3... | | | `-- Installing gstreamer-0.10.36_6... | | | `-- Extracting gstreamer-0.10.36_6: .......... done | | | `-- Installing gstreamer-plugins-0.10.36_8,3... | | | `-- Installing libXv-1.0.11,1... | | | | `-- Installing videoproto-2.3.3... | | | | `-- Extracting videoproto-2.3.3: ......... done | | | `-- Extracting libXv-1.0.11,1: .......... done | | | `-- Installing orc-0.4.25... | | | `-- Extracting orc-0.4.25: .......... done | | | `-- Extracting gstreamer-plugins-0.10.36_8,3: .......... done | | | `-- Installing qt4-declarative-4.8.7_1... | | | `-- Installing qt4-opengl-4.8.7_3... | | | `-- Extracting qt4-opengl-4.8.7_3: .......... done | | | `-- Installing qt4-script-4.8.7_3... | | | `-- Extracting qt4-script-4.8.7_3: .......... done | | | `-- Installing qt4-svg-4.8.7_2... | | | `-- Extracting qt4-svg-4.8.7_2: .......... done | | | `-- Installing qt4-xmlpatterns-4.8.7_2... | | | `-- Extracting qt4-xmlpatterns-4.8.7_2: .......... done | | | `-- Extracting qt4-declarative-4.8.7_1: .......... done | | `-- Extracting qt4-webkit-4.8.7_3: .......... done | | `-- Extracting qt4-assistant-4.8.7_1: ...... done | | `-- Installing qt4-qt3support-4.8.7_2... | | `-- Extracting qt4-qt3support-4.8.7_2: .......... done | `-- Extracting qt4-designer-4.8.7_1: .......... done `-- Extracting qscintilla2-2.10.3,1: .......... done Extracting py27-qt4-core-4.12.1_6,1: .......... done Message from qtchooser-39: qtchooser is a wrapper that allows selecting whether Qt4 or Qt5 binaries for qmake, moc and other tools will be run when invoking the binaries in $PATH. By default, the Qt5 versions are run. It is possible to change the behavior by setting the QT_SELECT environment variable to "qt4". See qtchooser(1) for more information. Message from qt4-corelib-4.8.7_11: ====================================================================== Qt 4 can be built with optional support for: - Common UNIX Printing System (CUPS) (enabled by default) - Network Audio System (NAS) - Qt style that renders using GTK (QGTKSTYLE) In order to enable them, you have to add QT4_OPTIONS= CUPS NAS QGTKSTYLE to your /etc/make.conf and compile devel/qt4-corelib and x11-toolkits/qt4-gui ports. Attention! Whenever you change the QT4_OPTIONS both devel/qt4-corelib and x11-toolkits/qt4-gui ports must be rebuilt! ====================================================================== Message from qt4-sql-4.8.7_2: ====================================================================== To enable Qt database support, install the database plugin ports. The following plugin ports are available: - databases/qt4-ibase-plugin InterBase/Firebird - databases/qt4-mysql-plugin MySQL - databases/qt4-odbc-plugin Open Database Connectivity - databases/qt4-pgsql-plugin PostgreSQL - databases/qt4-sqlite-plugin SQLite 2 - databases/qt4-sqlite3-plugin SQLite 3 ====================================================================== ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-qt4-core>=4.12.1 - found ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-qt4-gui>=4.12.1 - not found ===> Installing existing package /packages/All/py27-qt4-gui-4.12.1_2,1.txz Installing py27-qt4-gui-4.12.1_2,1... `-- Installing qt4-iconengines-4.8.7_2... `-- Extracting qt4-iconengines-4.8.7_2: .... done `-- Installing qt4-imageformats-4.8.7_2... | `-- Installing libmng-1.0.10_3... | | `-- Installing lcms-1.19_6,1... | | `-- Extracting lcms-1.19_6,1: .......... done | `-- Extracting libmng-1.0.10_3: ......... done `-- Extracting qt4-imageformats-4.8.7_2: .......... done `-- Installing qt4-inputmethods-4.8.7_2... `-- Extracting qt4-inputmethods-4.8.7_2: .... done Extracting py27-qt4-gui-4.12.1_2,1: .......... done ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-qt4-gui>=4.12.1 - found ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-qt4-test>=4.12.1 - not found ===> Installing existing package /packages/All/py27-qt4-test-4.12.1_2,1.txz Installing py27-qt4-test-4.12.1_2,1... `-- Installing qt4-testlib-4.8.7_2... `-- Extracting qt4-testlib-4.8.7_2: .......... done Extracting py27-qt4-test-4.12.1_2,1: .......... done ===> MOOSE-neural-simulator-3.1.2_1 depends on package: py27-qt4-test>=4.12.1 - found ===> Returning to build of MOOSE-neural-simulator-3.1.2_1 ===> MOOSE-neural-simulator-3.1.2_1 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for MOOSE-neural-simulator-3.1.2_1 ===> Generating temporary packing list /usr/local/bin/cmake -H/construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a -B/construction/science/MOOSE-neural-simulator/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/science/MOOSE-neural-simulator/.build/CMakeFiles /construction/science/MOOSE-neural-simulator/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f CMakeFiles/gui.dir/build.make CMakeFiles/gui.dir/depend cd /construction/science/MOOSE-neural-simulator/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build/CMakeFiles/gui.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/gui.dir/build.make CMakeFiles/gui.dir/build [ 50%] Building moose-gui /usr/local/bin/cmake -E copy_directory /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-gui /construction/science/MOOSE-neural-simulator/.build/__moose-gui_install /usr/local/bin/python2.7 -m compileall -q /construction/science/MOOSE-neural-simulator/.build/__moose-gui_install [ 50%] Built target gui /usr/bin/make -f CMakeFiles/examples.dir/build.make CMakeFiles/examples.dir/depend cd /construction/science/MOOSE-neural-simulator/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build/CMakeFiles/examples.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/examples.dir/build.make CMakeFiles/examples.dir/build /usr/local/bin/cmake -E copy_directory /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-examples /construction/science/MOOSE-neural-simulator/.build/__moose-examples_install /usr/local/bin/python2.7 -m compileall -q /construction/science/MOOSE-neural-simulator/.build/__moose-examples_install [ 50%] Built target examples /usr/bin/make -f CMakeFiles/moose-core.dir/build.make CMakeFiles/moose-core.dir/depend cd /construction/science/MOOSE-neural-simulator/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build/CMakeFiles/moose-core.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/moose-core.dir/build.make CMakeFiles/moose-core.dir/build [100%] Generating __moose-core_build/moose.bin MAKE=/usr/bin/make bash -c /construction/science/MOOSE-neural-simulator/.build/build_moose-core.sh + set -e + [ -z /usr/bin/make ] + echo 'Building MOOSE' Building MOOSE + export 'GSL_ROOT_DIR=' + export 'HDF5_ROOT=' + cd /construction/science/MOOSE-neural-simulator/.build/__moose-core_build + cmake '-DCMAKE_INSTALL_PREFIX=/construction/science/MOOSE-neural-simulator/.build/__moose-core_install' '-DCMAKE_BUILD_TYPE=Release' '-DWITH_BOOST=OFF' '-DPYTHON_EXECUTABLE=/usr/local/bin/python2.7' '-DMOOSE_VERSION=' /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a/moose-core -- Your compiler supports c++11 features. Enabling it -- MOOSE Version 3.2-git -- Operating system: DragonFly -- Building for Release/No unit tests. -- GSL version : 2.4 -- Found GSL /usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so -- HDF5: Using hdf5 compiler wrapper to determine CXX configuration -- MOOSE will use following HDF5 /usr/local/lib/libhdf5_cpp.so;/usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so;/usr/local/lib/libhdf5_hl_cpp.so;/usr/local/lib/libhdf5_hl.so -- Using gsl libraries: /usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so -- Checking for module 'muparser' -- Package 'muparser', required by 'virtual:world', not found -- Using private muparser -- Shared libs: /usr/local/lib/libhdf5_cpp.so;/usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so;/usr/local/lib/libhdf5_hl_cpp.so;/usr/local/lib/libhdf5_hl.so;/usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so -- Python so extension -- Python include flags: -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -- Platform DragonFly-5.0-SYNTH-x86_64-64bit-ELF ======================================= If cmake did not report any error, run 'make' to build MOOSE ======================================= -- Configuring done -- Generating done -- Build files have been written to: /construction/science/MOOSE-neural-simulator/.build/__moose-core_build + /usr/bin/make [ 3%] Built target muparser [ 12%] Built target basecode [ 16%] Built target msg [ 19%] Built target shell [ 26%] Built target randnum [ 27%] Built target scheduling [ 43%] Built target biophysics [ 52%] Built target moose_builtins [ 56%] Built target utility [ 61%] Built target mesh [ 62%] Built target moose_mpi [ 63%] Built target signeur [ 70%] Built target ksolve [ 75%] Built target hsolve [ 77%] Built target diffusion [ 79%] Built target device [ 81%] Built target benchmarks [ 88%] Built target kinetics [ 92%] Built target synapse [ 95%] Built target intfire [ 96%] Built target libmoose [ 97%] Copying required python files and other files to build directory [ 97%] Built target copy_python_files [100%] Built target _moose + ctest -output-on-failure Test project /construction/science/MOOSE-neural-simulator/.build/__moose-core_build Start 1: test_accessing_existing_paths 1/24 Test #1: test_accessing_existing_paths .... Passed 1.57 sec Start 2: test_connectionLists 2/24 Test #2: test_connectionLists ............. Passed 3.45 sec Start 3: test_difshells 3/24 Test #3: test_difshells ...................***Failed 5.23 sec Start 4: test_docs 4/24 Test #4: test_docs ........................ Passed 0.98 sec Start 5: test_function 5/24 Test #5: test_function .................... Passed 0.92 sec Start 6: test_hsolve_externalCalcium 6/24 Test #6: test_hsolve_externalCalcium ......***Failed 1.94 sec Start 7: test_import 7/24 Test #7: test_import ......................***Failed 1.37 sec Start 8: test_kkit 8/24 Test #8: test_kkit ........................ Passed 2.43 sec Start 9: test_ksolve 9/24 Test #9: test_ksolve ...................... Passed 0.52 sec Start 10: test_moose_paths 10/24 Test #10: test_moose_paths ................. Passed 0.43 sec Start 11: test_muparser 11/24 Test #11: test_muparser ....................***Failed 1.49 sec Start 12: test_neuroml 12/24 Test #12: test_neuroml .....................***Failed 1.14 sec Start 13: test_nsdf 13/24 Test #13: test_nsdf ........................ Passed 1.25 sec Start 14: test_paths 14/24 Test #14: test_paths ....................... Passed 1.14 sec Start 15: test_pymoose 15/24 Test #15: test_pymoose ..................... Passed 1.09 sec Start 16: test_pyrun 16/24 Test #16: test_pyrun ....................... Passed 0.60 sec Start 17: test_rdesigneur 17/24 Test #17: test_rdesigneur ..................***Failed 3.02 sec Start 18: test_sbml 18/24 Test #18: test_sbml ........................***Failed 1.49 sec Start 19: test_snippets 19/24 Test #19: test_snippets .................... Passed 0.04 sec Start 20: test_streamer 20/24 Test #20: test_streamer .................... Passed 1.24 sec Start 21: test_synchan 21/24 Test #21: test_synchan ..................... Passed 0.47 sec Start 22: test_table_streaming_support 22/24 Test #22: test_table_streaming_support ..... Passed 0.75 sec Start 23: test_utils 23/24 Test #23: test_utils .......................***Failed 1.74 sec Start 24: test_vec 24/24 Test #24: test_vec ......................... Passed 1.14 sec 67% tests passed, 8 tests failed out of 24 Total Test time (real) = 35.47 sec The following tests FAILED: 3 - test_difshells (Failed) 6 - test_hsolve_externalCalcium (Failed) 7 - test_import (Failed) 11 - test_muparser (Failed) 12 - test_neuroml (Failed) 17 - test_rdesigneur (Failed) 18 - test_sbml (Failed) 23 - test_utils (Failed) Errors while running CTest + echo 'Some tests failed' Some tests failed + /usr/bin/make install [ 3%] Built target muparser [ 12%] Built target basecode [ 16%] Built target msg [ 19%] Built target shell [ 26%] Built target randnum [ 27%] Built target scheduling [ 43%] Built target biophysics [ 52%] Built target moose_builtins [ 56%] Built target utility [ 61%] Built target mesh [ 62%] Built target moose_mpi [ 63%] Built target signeur [ 70%] Built target ksolve [ 75%] Built target hsolve [ 77%] Built target diffusion [ 79%] Built target device [ 81%] Built target benchmarks [ 88%] Built target kinetics [ 92%] Built target synapse [ 95%] Built target intfire [ 96%] Built target libmoose [ 97%] Copying required python files and other files to build directory [ 97%] Built target copy_python_files [100%] Built target _moose Install the project... -- Install configuration: "Release" Failed to read VERSION [Errno 2] No such file or directory: '/construction/science/MOOSE-neural-simulator/.build/__moose-core_build/python/../VERSION' Using default 3.2.git [WARN] Failed to determine importlib suffix running install running build running build_py copying rdesigneur/rmoogli.py -> build/lib/rdesigneur copying rdesigneur/rdesigneurProtos.py -> build/lib/rdesigneur copying rdesigneur/__init__.py -> build/lib/rdesigneur copying rdesigneur/rdesigneur.py -> build/lib/rdesigneur copying moose/constants.py -> build/lib/moose copying moose/OrderedDict.py -> build/lib/moose copying moose/methods_utils.py -> build/lib/moose copying moose/alternate.py -> build/lib/moose copying moose/print_utils.py -> build/lib/moose copying moose/hdfutil.py -> build/lib/moose copying moose/utils.py -> build/lib/moose copying moose/optimizer_interface.py -> build/lib/moose copying moose/moose_test.py -> build/lib/moose copying moose/graph_utils.py -> build/lib/moose copying moose/moose_constants.py -> build/lib/moose copying moose/recording.py -> build/lib/moose copying moose/graphutil.py -> build/lib/moose copying moose/plot_utils.py -> build/lib/moose copying moose/moose.py -> build/lib/moose copying moose/__init__.py -> build/lib/moose copying moose/moose_config.py -> build/lib/moose copying moose/SBML/readSBML.py -> build/lib/moose/SBML copying moose/SBML/__init__.py -> build/lib/moose/SBML copying moose/SBML/writeSBML.py -> build/lib/moose/SBML copying moose/SBML/validation.py -> build/lib/moose/SBML copying moose/neuroml/ChannelML.py -> build/lib/moose/neuroml copying moose/neuroml/__init__.py -> build/lib/moose/neuroml copying moose/neuroml/MorphML.py -> build/lib/moose/neuroml copying moose/neuroml/NeuroML.py -> build/lib/moose/neuroml copying moose/neuroml/NetworkML.py -> build/lib/moose/neuroml copying moose/neuroml/utils.py -> build/lib/moose/neuroml copying moose/genesis/__init__.py -> build/lib/moose/genesis copying moose/genesis/writeKkit.py -> build/lib/moose/genesis copying moose/chemUtil/graphUtils.py -> build/lib/moose/chemUtil copying moose/chemUtil/add_Delete_ChemicalSolver.py -> build/lib/moose/chemUtil copying moose/chemUtil/chemConnectUtil.py -> build/lib/moose/chemUtil copying moose/chemUtil/__init__.py -> build/lib/moose/chemUtil copying moose/chemMerge/merge.py -> build/lib/moose/chemMerge copying moose/chemMerge/__init__.py -> build/lib/moose/chemMerge copying moose/chemMerge/mtypes.py -> build/lib/moose/chemMerge running install_lib copying build/lib/moose/chemMerge/mtypes.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge copying build/lib/moose/chemMerge/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge copying build/lib/moose/chemMerge/merge.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge copying build/lib/moose/chemUtil/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil copying build/lib/moose/chemUtil/chemConnectUtil.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil copying build/lib/moose/chemUtil/add_Delete_ChemicalSolver.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil copying build/lib/moose/chemUtil/graphUtils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil copying build/lib/moose/genesis/writeKkit.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/genesis copying build/lib/moose/genesis/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/genesis copying build/lib/moose/neuroml/utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/NetworkML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/NeuroML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/MorphML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/neuroml/ChannelML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml copying build/lib/moose/SBML/validation.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML copying build/lib/moose/SBML/writeSBML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML copying build/lib/moose/SBML/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML copying build/lib/moose/SBML/readSBML.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML copying build/lib/moose/moose_config.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/moose.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/plot_utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/graphutil.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/recording.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/moose_constants.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/graph_utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/moose_test.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/optimizer_interface.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/hdfutil.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/print_utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/alternate.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/methods_utils.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/OrderedDict.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/moose/constants.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose copying build/lib/rdesigneur/rdesigneur.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur copying build/lib/rdesigneur/__init__.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur copying build/lib/rdesigneur/rdesigneurProtos.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur copying build/lib/rdesigneur/rmoogli.py -> /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge/mtypes.py to mtypes.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemMerge/merge.py to merge.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil/chemConnectUtil.py to chemConnectUtil.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil/add_Delete_ChemicalSolver.py to add_Delete_ChemicalSolver.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/chemUtil/graphUtils.py to graphUtils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/genesis/writeKkit.py to writeKkit.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/genesis/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/utils.py to utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/NetworkML.py to NetworkML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/NeuroML.py to NeuroML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/MorphML.py to MorphML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/neuroml/ChannelML.py to ChannelML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML/validation.py to validation.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML/writeSBML.py to writeSBML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/SBML/readSBML.py to readSBML.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/moose_config.py to moose_config.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/moose.py to moose.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/plot_utils.py to plot_utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/graphutil.py to graphutil.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/recording.py to recording.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/moose_constants.py to moose_constants.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/graph_utils.py to graph_utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/moose_test.py to moose_test.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/optimizer_interface.py to optimizer_interface.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/utils.py to utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/hdfutil.py to hdfutil.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/print_utils.py to print_utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/alternate.py to alternate.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/methods_utils.py to methods_utils.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/OrderedDict.py to OrderedDict.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose/constants.py to constants.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur/rdesigneur.py to rdesigneur.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur/__init__.py to __init__.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur/rdesigneurProtos.py to rdesigneurProtos.pyc byte-compiling /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/rdesigneur/rmoogli.py to rmoogli.pyc running install_egg_info Removing /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose-3.2.git-py2.7.egg-info Writing /construction/science/MOOSE-neural-simulator/.build/__moose-core_install/lib/python2.7/site-packages/moose-3.2.git-py2.7.egg-info [100%] Built target moose-core /usr/bin/make -f CMakeFiles/moose.dir/build.make CMakeFiles/moose.dir/depend cd /construction/science/MOOSE-neural-simulator/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/moose-3.1.2-382-gc93d23a /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build /construction/science/MOOSE-neural-simulator/.build/CMakeFiles/moose.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/moose.dir/build.make CMakeFiles/moose.dir/build [100%] Built target moose /usr/local/bin/cmake -E cmake_progress_start /construction/science/MOOSE-neural-simulator/.build/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /construction/science/MOOSE-neural-simulator/stage/usr/local -- Up-to-date: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7 -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/rdesigneur -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/rdesigneur/rmoogli.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/rdesigneur/rdesigneurProtos.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/rdesigneur/__init__.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/rdesigneur/rdesigneur.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/constants.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/OrderedDict.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/methods_utils.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/alternate.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/print_utils.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/hdfutil.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/utils.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/optimizer_interface.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/moose_test.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/graph_utils.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/moose_constants.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/recording.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/graphutil.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/plot_utils.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/moose.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/__init__.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/moose_config.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/SBML -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/SBML/readSBML.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/SBML/__init__.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/SBML/writeSBML.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/SBML/validation.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/neuroml -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/neuroml/ChannelML.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/neuroml/__init__.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/neuroml/MorphML.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/neuroml/NeuroML.py -- Installing: /construction/science/MOOSE-neural-simulator/stage/usr/local/lib/python2.7/site-packages/moose/neuroml/NetworkML.py -- Installing: 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