build.log

build.log (text/x-log), 63.67 KB, created by Juergen Rose on 2017-12-18 00:58:26 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]
[32;01m * [39;49;00mUSE:        abi_x86_64 amd64 doc elibc_glibc examples fetk iapbs kernel_linux openmp python python_targets_python2_7 tools userland_GNU
[32;01m * [39;49;00mFEATURES:   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/lib64 -DLIBRARY_INSTALL_PATH=lib64 -DFETK_PATH=/usr/ -DBUILD_SHARED_LIBS=ON -DENABLE_QUIT=OFF -DBUILD_DOC=ON -DBUILD_TOOLS=ON -DENABLE_BEM=OFF -DENABLE_DEBUG=OFF -DENABLE_VERBOSE_DEBUG=OFF -DENABLE_FAST=OFF -DENABLE_FETK=ON -DENABLE_MPI=OFF -DENABLE_PYTHON=ON -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
Re-run cmake no build system arguments
-- The C compiler identification is GNU 7.2.0
-- The CXX compiler identification is GNU 7.2.0
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- 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/x86_64-pc-linux-gnu-g++
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - 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
-- External maloc headers found
-- Checking for fetk components
-- Inline functions enabled
-- Looking for python components
-- Found PythonInterp: /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/temp/python2.7/bin/python (found version "2.7.14") 
-- Found PythonLibs: /usr/lib/libpython2.7.so (found version "2.7.14") 
-- Checking for OpenMP
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- OpenMP support enabled
libs: -lmaloc-lm-lstdc++-L/usr/lib64-lamd-lpunc-lmc-lgamer-lsuperlu-lumfpack-lf77blas-lvf2c-ltetgen-ltriangle-lreadline-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;-lstdc++;-L/usr/lib64;-lamd;-lpunc;-lmc;-lgamer;-lsuperlu;-lumfpack;-lf77blas;-lvf2c;-ltetgen;-ltriangle;-lreadline;-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;-lstdc++;-L/usr/lib64;-lamd;-lpunc;-lmc;-lgamer;-lsuperlu;-lumfpack;-lf77blas;-lvf2c;-ltetgen;-ltriangle;-lreadline;-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;-lstdc++;-L/usr/lib64;-lamd;-lpunc;-lmc;-lgamer;-lsuperlu;-lumfpack;-lf77blas;-lvf2c;-ltetgen;-ltriangle;-lreadline;-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;-lstdc++;-L/usr/lib64;-lamd;-lpunc;-lmc;-lgamer;-lsuperlu;-lumfpack;-lf77blas;-lvf2c;-ltetgen;-ltriangle;-lreadline;-fopenmp
-- Added apbs_geoflow
-- Adding apbs_fem
-- With source files vcsm.c;vfetk.c;vpee.c
-- With external header files vcsm.h;vfetk.h;vpee.h
-- With internal header files 
-- With library dependencies -lmaloc;-lm;-lstdc++;-L/usr/lib64;-lamd;-lpunc;-lmc;-lgamer;-lsuperlu;-lumfpack;-lf77blas;-lvf2c;-ltetgen;-ltriangle;-lreadline;-fopenmp;apbs_geoflow
-- Added apbs_fem
-- 
--  
-- -lmaloc;-lm;-lstdc++;-L/usr/lib64;-lamd;-lpunc;-lmc;-lgamer;-lsuperlu;-lumfpack;-lf77blas;-lvf2c;-ltetgen;-ltriangle;-lreadline;-fopenmp apbs_generic;apbs_pmgc;apbs_mg;apbs_geoflow;apbs_fem
--  
-- -std=c99
-- Building documentation enabled
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components:  doxygen dot 
-- Supplemental tools enabled
-- Building mesh
-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem
-- Building manip
-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem
-- Building of iAPBS interface enabled
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -std=c99
C++             -march=broadwell -O2 -pipe
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 -j9 -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=
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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[0m
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[  2%] [32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/modules.cpp.o[0m
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cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/bin/x86_64-pc-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/usr/include/maloc -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src   -I/usr/include/eigen3 -DNDEBUG -march=broadwell -O2 -pipe -fPIC   -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
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[  5%] [32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/subfunction.cpp.o[0m
cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/bin/x86_64-pc-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/usr/include/maloc -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src   -I/usr/include/eigen3 -DNDEBUG -march=broadwell -O2 -pipe -fPIC   -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
[  6%] [32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/surfconcz.cpp.o[0m
cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/bin/x86_64-pc-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/usr/include/maloc -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src   -I/usr/include/eigen3 -DNDEBUG -march=broadwell -O2 -pipe -fPIC   -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
[  7%] [32m[1mLinking CXX shared library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_geoflow.so[0m
cd /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/bin/x86_64-pc-linux-gnu-g++ -fPIC -march=broadwell -O2 -pipe -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 -lstdc++ -L/usr/lib64 -lamd -lpunc -lmc -lgamer -lsuperlu -lumfpack -lf77blas -lvf2c -ltetgen -ltriangle -lreadline -fopenmp 
make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build'
[  7%] Built target apbs_geoflow
make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/depend
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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/fem /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/fem /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake --color=
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[35m[1mScanning dependencies of target apbs_fem[0m
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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/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=
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cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/doc/programmer/latex && make
/bin/sh: line 0: cd: /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/doc/programmer/latex: No such file or directory
make[2]: *** [doc/CMakeFiles/doc-pdf.dir/build.make:58: doc/CMakeFiles/doc-pdf] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build'
make[1]: *** [CMakeFiles/Makefile2:481: doc/CMakeFiles/doc-pdf.dir/all] Error 2
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build'
make: *** [Makefile:130: 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/sci-chemistry:apbs-1.4.1-r2:20171218-004311.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'