build.log

c6dd27256017.txt (text/plain), 61.47 KB, created by Pacho Ramos on 2015-05-07 18:11:38 UTC

[32;01m * [39;49;00mPackage:    sci-chemistry/apbs-1.4.1-r2
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail] [e-mail]
[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 -j1 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[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=
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".
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[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/surfconcz.cpp.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow/surfconcz.cpp
[31m[1mLinking CXX shared library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_geoflow.so
[0mcd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_geoflow.dir/link.txt --verbose=1
/usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++  -fPIC -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector   -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libapbs_geoflow.so -o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_geoflow.so CMakeFiles/apbs_geoflow.dir/cpbconcz2.cpp.o CMakeFiles/apbs_geoflow.dir/modules.cpp.o CMakeFiles/apbs_geoflow.dir/pbsolvercz.cpp.o CMakeFiles/apbs_geoflow.dir/solvationsub.cpp.o CMakeFiles/apbs_geoflow.dir/subfunction.cpp.o CMakeFiles/apbs_geoflow.dir/surfconcz.cpp.o -lmaloc -lm -fopenmp 
make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build'
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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=
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