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Gentoo's Bugzilla – Attachment 402048 Details for
Bug 547816
sci-chemistry/apbs-1.4.1-r2 fails to build on ppc
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build.log
9e4633f108a8.txt (text/plain), 65.61 KB, created by
Pacho Ramos
on 2015-04-26 14:02:12 UTC
(
hide
)
Description:
build.log
Filename:
MIME Type:
Creator:
Pacho Ramos
Created:
2015-04-26 14:02:12 UTC
Size:
65.61 KB
patch
obsolete
>[32;01m * [39;49;00mPackage: sci-chemistry/apbs-1.4.1-r2 >[32;01m * [39;49;00mRepository: gentoo >[32;01m * [39;49;00mMaintainer: jlec@gentoo.org sci-chemistry@gentoo.org >[32;01m * [39;49;00mUSE: abi_ppc_32 elibc_glibc kernel_linux openmp ppc python_targets_python2_7 userland_GNU >[32;01m * [39;49;00mFEATURES: 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 ... > [32;01m*[0m Applying apbs-1.4.1-multilib.patch ... >[A[142C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying apbs-1.4.1-manip.patch ... >[A[142C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying apbs-1.4.1-python.patch ... >[A[142C [34;01m[ [32;01mok[34;01m ][0m >>>> 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". >[35m[1mScanning 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". >[35m[1mScanning 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". >[35m[1mScanning dependencies of target apbs_generic >[0mmake[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%] [0mmake[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 >[32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/modules.cpp.o >[0mcd /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 >[32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/cpbconcz2.cpp.o >[0m[32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/pbsolvercz.cpp.o >[0mcd /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 >[0m[32mBuilding 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 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'/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >[32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/surfconcz.cpp.o >[32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/solvationsub.cpp.o >[0m[0mmake -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 /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow/surfconcz.cpp >cd 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-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 âsetupStringâ: >/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 âgetpidâ [-Wimplicit-function-declaration] > sprintf(string, "%swrite pot dx iapbs-pot-%d\n", string, getpid()); > ^ >[31m[1mLinking C static library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libiapbs.a >[0mcd 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/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 âVgrid_readDXâ: >/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/mg/vgrid.c:749:5: warning: format â%luâ expects argument of type âlong unsigned int *â, but argument 3 has type âsize_t *â [-Wformat=] > VJMPERR1(1 == sscanf(tok, "%lu", &itmp)); > ^ >[31m[1mLinking C shared library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_mg.so >[0mcd /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". >[35m[1mScanning dependencies of target apbs_routines >[35m[1mScanning dependencies of target apbs >[0m[0mmake[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%] [32mBuilding C object src/CMakeFiles/apbs_routines.dir/routines.c.o >[32mBuilding C object src/CMakeFiles/apbs.dir/routines.c.o >[0m[0m[32mBuilding C object src/CMakeFiles/apbs.dir/main.c.o >[0mcd /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 >[31m[1mLinking C executable /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/bin/apbs >[0mcd /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 >[31m[1mLinking C shared library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_routines.so >[0mcd /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 > [31;01m*[0m ERROR: sci-chemistry/apbs-1.4.1-r2::gentoo failed (compile phase): > [31;01m*[0m emake failed > [31;01m*[0m > [31;01m*[0m If you need support, post the output of `emerge --info '=sci-chemistry/apbs-1.4.1-r2::gentoo'`, > [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-chemistry/apbs-1.4.1-r2::gentoo'`. > [31;01m*[0m The complete build log is located at '/var/log/portage/build/sci-chemistry/apbs-1.4.1-r2:20150426-135114.log'. > [31;01m*[0m For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/temp/build.log'. > [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/temp/environment'. > [31;01m*[0m Working directory: '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' > [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs'
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