* Package: sci-chemistry/apbs-1.4.1-r2  * Repository: gentoo  * Maintainer: jlec@gentoo.org sci-chemistry@gentoo.org  * USE: abi_ppc_32 elibc_glibc kernel_linux openmp ppc python_targets_python2_7 userland_GNU  * FEATURES: ccache preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking apbs-1.4.1.zip to /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work >>> Preparing source in /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs ... * Applying apbs-1.4.1-multilib.patch ...  [ ok ] * Applying apbs-1.4.1-manip.patch ...  [ ok ] * Applying apbs-1.4.1-python.patch ...  [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build" cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_SKIP_RPATH=ON -DTOOLS_PATH=/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/image//usr -DSYS_LIBPATHS=/usr/lib -DLIBRARY_INSTALL_PATH=lib -DFETK_PATH=/usr/ -DBUILD_SHARED_LIBS=ON -DENABLE_QUIT=OFF -DBUILD_DOC=OFF -DBUILD_TOOLS=OFF -DENABLE_BEM=OFF -DENABLE_DEBUG=OFF -DENABLE_VERBOSE_DEBUG=OFF -DENABLE_FAST=OFF -DENABLE_FETK=OFF -DENABLE_MPI=OFF -DENABLE_PYTHON=OFF -DENABLE_iAPBS=ON -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs Not searching for unused variables given on the command line. loading initial cache file /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/gentoo_common_config.cmake -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- Check for working C compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -- Check for working C compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -- Check for working CXX compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Found fetk: /usr -- External maloc library was found: /usr/lib/libmaloc.so -- Looking for include file maloc/maloc.h -- Looking for include file maloc/maloc.h - found -- External maloc headers found -- Inline functions enabled -- Checking for OpenMP -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- OpenMP support enabled libs: -lmaloc-lm-fopenmp -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies -lmaloc;-lm;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies -lmaloc;-lm;-fopenmp;apbs_geoflow -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies -lmaloc;-lm;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_geoflow -- With source files cpbconcz2.cpp;modules.cpp;pbsolvercz.cpp;solvationsub.cpp;subfunction.cpp;surfconcz.cpp -- With external header files cpbconcz2.h -- With internal header files -- With library dependencies -lmaloc;-lm;-fopenmp -- Added apbs_geoflow -- -- -- -lmaloc;-lm;-fopenmp apbs_generic;apbs_pmgc;apbs_mg;apbs_geoflow -- -- -std=c99 -- Building of iAPBS interface enabled -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -std=c99 C++ -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector Linker flags: Executable -Wl,-O1 -Wl,--as-needed Module -Wl,-O1 -Wl,--as-needed Shared -Wl,-O1 -Wl,--as-needed -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build" make -j33 VERBOSE=1 /usr/bin/cmake -H/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs -B/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' make -f src/geoflow/CMakeFiles/apbs_geoflow.dir/build.make src/geoflow/CMakeFiles/apbs_geoflow.dir/depend make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make -f contrib/iapbs/src/CMakeFiles/iapbs.dir/build.make contrib/iapbs/src/CMakeFiles/iapbs.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/contrib/iapbs/src /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/contrib/iapbs/src /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/contrib/iapbs/src/CMakeFiles/iapbs.dir/DependInfo.cmake --color= make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow/CMakeFiles/apbs_geoflow.dir/DependInfo.cmake --color= make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/generic /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake --color= Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow/CMakeFiles/apbs_geoflow.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow/CMakeFiles/apbs_geoflow.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow/CMakeFiles/apbs_geoflow.dir/depend.internal". Scanning dependencies of target apbs_geoflow Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/contrib/iapbs/src/CMakeFiles/iapbs.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/contrib/iapbs/src/CMakeFiles/iapbs.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/contrib/iapbs/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/contrib/iapbs/src/CMakeFiles/iapbs.dir/depend.internal". Scanning dependencies of target iapbs Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic/CMakeFiles/apbs_generic.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic/CMakeFiles/apbs_generic.dir/depend.internal". Scanning dependencies of target apbs_generic make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' make -f src/geoflow/CMakeFiles/apbs_geoflow.dir/build.make src/geoflow/CMakeFiles/apbs_geoflow.dir/build make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 19 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 20 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 21 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 22 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 23 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 24 [ 2%] [ 4%] [ 6%] [ 8%] [ 10%] [ 12%] make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' make -f contrib/iapbs/src/CMakeFiles/iapbs.dir/build.make contrib/iapbs/src/CMakeFiles/iapbs.dir/build Building CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/modules.cpp.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/usr/include/eigen3 -DNDEBUG -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -std=c++0x -o CMakeFiles/apbs_geoflow.dir/modules.cpp.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow/modules.cpp Building CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/cpbconcz2.cpp.o Building CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/pbsolvercz.cpp.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/usr/include/eigen3 -DNDEBUG -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -std=c++0x -o CMakeFiles/apbs_geoflow.dir/cpbconcz2.cpp.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow/cpbconcz2.cpp Building CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/subfunction.cpp.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/usr/include/eigen3 -DNDEBUG -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -std=c++0x -o CMakeFiles/apbs_geoflow.dir/pbsolvercz.cpp.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow/pbsolvercz.cpp make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 49 cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/usr/include/eigen3 -DNDEBUG -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -std=c++0x -o CMakeFiles/apbs_geoflow.dir/subfunction.cpp.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow/subfunction.cpp make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' Building CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/surfconcz.cpp.o Building CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/solvationsub.cpp.o make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/usr/include/eigen3 -DNDEBUG -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -std=c++0x -o CMakeFiles/apbs_geoflow.dir/surfconcz.cpp.o -c 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/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/generic/vstring.c Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_generic_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_generic.dir/vparam.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/generic/vparam.c cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_generic_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_generic.dir/vgreen.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/generic/vgreen.c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/contrib/iapbs/src/apbs_driver.c: In function ‘setupString’: /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/contrib/iapbs/src/apbs_driver.c:938:7: warning: implicit declaration of function ‘getpid’ [-Wimplicit-function-declaration] sprintf(string, "%swrite pot dx iapbs-pot-%d\n", string, getpid()); ^ Linking C static library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libiapbs.a cd 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/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/generic/nosh.c: In function ‘NOsh_calc_copy’: /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/generic/nosh.c:432:9: warning: implicit declaration of function ‘BEMparm_copy’ [-Wimplicit-function-declaration] BEMparm_copy(thee->bemparm, source->bemparm); ^ Linking C shared library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_generic.so cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -fPIC -std=c99 -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libapbs_generic.so -o 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make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 19 20 21 22 23 24 [ 46%] Built target apbs_geoflow make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/pmgc /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/pmgc 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/usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_pmgc_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/pmgc/mgdrvd.c Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/pmgc && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_pmgc_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c 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CMakeFiles/apbs_pmgc.dir/newtond.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/pmgc/newtond.c Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/pmgc && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_pmgc_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/pmgc/mgsubd.c Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/pmgc && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_pmgc_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/pmgc/newdrvd.c Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/pmgc && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_pmgc_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_pmgc.dir/powerd.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/pmgc/powerd.c cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/pmgc && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_pmgc_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_pmgc.dir/smoothd.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/pmgc/smoothd.c Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/pmgc && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_pmgc_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/pmgc/mgfasd.c Linking C shared library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_pmgc.so cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/pmgc && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pmgc.dir/link.txt --verbose=1 /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -fPIC -std=c99 -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libapbs_pmgc.so -o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_pmgc.so CMakeFiles/apbs_pmgc.dir/buildAd.c.o CMakeFiles/apbs_pmgc.dir/buildBd.c.o CMakeFiles/apbs_pmgc.dir/buildGd.c.o CMakeFiles/apbs_pmgc.dir/buildPd.c.o CMakeFiles/apbs_pmgc.dir/cgd.c.o CMakeFiles/apbs_pmgc.dir/gsd.c.o CMakeFiles/apbs_pmgc.dir/matvecd.c.o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -lmaloc -lm -fopenmp /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_geoflow.so -lmaloc -lm -fopenmp make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 [ 83%] Built target apbs_pmgc make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/mg /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake --color= Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg/CMakeFiles/apbs_mg.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg/CMakeFiles/apbs_mg.dir/depend.internal". Scanning dependencies of target apbs_mg make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 25 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 26 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 27 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 28 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 29 [ 85%] [ 87%] [ 89%] [ 91%] [ 93%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_mg_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_mg.dir/vopot.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/mg/vopot.c Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_mg_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_mg.dir/vgrid.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/mg/vgrid.c Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_mg_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_mg.dir/vmgrid.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/mg/vmgrid.c cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_mg_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_mg.dir/vpmg.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/mg/vpmg.c cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_mg_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_mg.dir/vpmgp.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/mg/vpmgp.c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/mg/vgrid.c: In function ‘Vgrid_readDX’: /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/mg/vgrid.c:749:5: warning: format ‘%lu’ expects argument of type ‘long unsigned int *’, but argument 3 has type ‘size_t *’ [-Wformat=] VJMPERR1(1 == sscanf(tok, "%lu", &itmp)); ^ Linking C shared library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_mg.so cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_mg.dir/link.txt --verbose=1 /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -fPIC -std=c99 -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libapbs_mg.so -o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_mg.so CMakeFiles/apbs_mg.dir/vgrid.c.o CMakeFiles/apbs_mg.dir/vmgrid.c.o CMakeFiles/apbs_mg.dir/vopot.c.o CMakeFiles/apbs_mg.dir/vpmg.c.o CMakeFiles/apbs_mg.dir/vpmgp.c.o -lmaloc -lm -fopenmp /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_generic.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_pmgc.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_geoflow.so -lmaloc -lm -fopenmp make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 25 26 27 28 29 [ 93%] Built target apbs_mg make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/CMakeFiles/apbs.dir/DependInfo.cmake --color= make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake --color= Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/CMakeFiles/apbs.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/CMakeFiles/apbs.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/CMakeFiles/apbs_routines.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/CMakeFiles/apbs_routines.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/CMakeFiles/apbs.dir/depend.internal". Scanning dependencies of target apbs_routines Scanning dependencies of target apbs make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 1 make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 48 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 2 [ 97%] [ 97%] [100%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o Building C object src/CMakeFiles/apbs.dir/routines.c.o Building C object src/CMakeFiles/apbs.dir/main.c.o cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -I/usr/include/eigen3 -DNDEBUG -std=c99 -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs.dir/routines.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/routines.c cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_routines_EXPORTS -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs_routines.dir/routines.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/routines.c cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -I/usr/include/eigen3 -DNDEBUG -std=c99 -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -fopenmp -o CMakeFiles/apbs.dir/main.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/main.c Linking C executable /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/bin/apbs cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1 /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -std=c99 -Wl,-O1 -Wl,--as-needed CMakeFiles/apbs.dir/main.c.o CMakeFiles/apbs.dir/routines.c.o -o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/bin/apbs -rdynamic -lmaloc -lm -fopenmp /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_generic.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_pmgc.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_mg.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_geoflow.so -lmaloc -lm -fopenmp /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_generic.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_pmgc.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_geoflow.so -lmaloc -lm -fopenmp Linking C shared library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_routines.so cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1 /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -fPIC -std=c99 -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so -o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_routines.so CMakeFiles/apbs_routines.dir/routines.c.o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_mg.so -lapbs_fem /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_generic.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_pmgc.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_geoflow.so -lmaloc -lm -fopenmp /usr/lib/gcc/powerpc-unknown-linux-gnu/4.8.4/../../../../powerpc-unknown-linux-gnu/bin/ld: cannot find -lapbs_fem make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles 1 2 collect2: error: ld returned 1 exit status src/CMakeFiles/apbs_routines.dir/build.make:92: recipe for target '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_routines.so' failed make[2]: *** [/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_routines.so] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' CMakeFiles/Makefile2:132: recipe for target 'src/CMakeFiles/apbs_routines.dir/all' failed make[1]: *** [src/CMakeFiles/apbs_routines.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... [100%] Built target apbs make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' Makefile:116: recipe for target 'all' failed make: *** [all] Error 2 * ERROR: sci-chemistry/apbs-1.4.1-r2::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-chemistry/apbs-1.4.1-r2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/apbs-1.4.1-r2::gentoo'`. * The complete build log is located at '/var/log/portage/build/sci-chemistry/apbs-1.4.1-r2:20150426-135114.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' * S: '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs'