* Package: dev-python/graph-tool-2.27 * Repository: gentoo * Maintainer: python@gentoo.org horea.christ@gmail.com * USE: abi_x86_64 amd64 cairo elibc_glibc kernel_linux openmp python_targets_python2_7 python_targets_python3_6 python_targets_python3_7 userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking graph-tool-2.27.tar.bz2 to /var/tmp/portage/dev-python/graph-tool-2.27/work >>> Source unpacked in /var/tmp/portage/dev-python/graph-tool-2.27/work >>> Preparing source in /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27 ... * Will copy sources from /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27 * python2_7: copying to /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7 * python3_6: copying to /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python3_6 * python3_7: copying to /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python3_7 >>> Source prepared. >>> Configuring source in /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27 ... * python2_7: running run_in_build_dir configure * econf: updating graph-tool-2.27-python3_7/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27-python3_7/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.27-python3_6/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27-python3_6/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.27-python2_7/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27-python2_7/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.27/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27/build-aux/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/graph-tool-2.27 --htmldir=/usr/share/doc/graph-tool-2.27/html --with-sysroot=/ --libdir=/usr/lib64 --disable-static --enable-openmp --enable-cairo --with-boost-python=boost_python27 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/lib/portage/python3.7/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking whether make supports nested variables... 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BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for archiver @FILE support... @ checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok checking for sysroot... / checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-pc-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... 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description... graph-tool Python library checking our pkgconfig requires... checking our pkgconfig ext libs... -L/usr/lib64 -lpython2.7 -lboost_python27 checking our pkgconfig cppflags... -I/usr/lib64/python2.7/site-packages/graph_tool/include -I/usr/lib64/python2.7/site-packages/graph_tool/include/boost-workaround -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include checking our pkgconfig ldflags... noninstalled pkgconfig -L /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7/src/.libs noninstalled pkgconfig -I /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7/. checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/graph/Makefile config.status: creating src/graph/centrality/Makefile config.status: creating src/graph/clustering/Makefile 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================================================================================(B  CONFIGURATION SUMMARY (B ================================================================================(B Using python version: 2.7.16(B Python interpreter: /usr/bin/python2.7(B Installation path: /usr/lib64/python2.7/site-packages/graph_tool(B C++ compiler (CXX): x86_64-pc-linux-gnu-g++(B C++ compiler version: 9.2.0(B Prefix: /usr(B Pkgconfigdir: ${libdir}/pkgconfig(B Python CPP flags: -I/usr/include/python2.7(B Python LD flags: -L/usr/lib64 -lpython2.7(B Boost CPP flags: -pthread -I/usr/include(B Boost LD flags: -lboost_iostreams-mt -lboost_python27 -lboost_regex-mt -lboost_coroutine-mt(B Numpy CPP flags: -I/usr/lib64/python2.7/site-packages/numpy/core/include(B Sparsehash CPP flags: (B CGAL CPP flags: -I/usr/include(B CGAL LD flags: -L/usr/lib -lCGAL -lCGAL_Core -lgmp -lboost_thread -lpthread(B Expat CPP flags: -I/usr/include(B Expat LD flags: -L/usr/lib -lexpat(B Cairomm CPP flags: -I/usr/include/cairomm-1.0 -I/usr/lib64/cairomm-1.0/include -I/usr/include/cairo -I/usr/lib64/libffi-3.3_rc0/include -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libdrm -I/usr/include/libpng16 -I/usr/include/sigc++-2.0 -I/usr/lib64/sigc++-2.0/include(B Cairomm LD flags: -lcairomm-1.0 -lcairo -lsigc-2.0(B OpenMP compiler flags: -fopenmp(B OpenMP LD flags: (B Extra CPPFLAGS: -DNDEBUG (B Extra CXXFLAGS: -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4(B Extra LDFLAGS: -Wl,-O1 -Wl,--as-needed(B Using OpenMP: yes(B Using sparsehash: yes(B Using cairo: yes(B ================================================================================(B * python3_6: running run_in_build_dir configure * econf: updating graph-tool-2.27-python3_7/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.27-python3_7/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27-python3_6/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.27-python3_6/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27-python2_7/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.27-python2_7/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.27/build-aux/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/graph-tool-2.27 --htmldir=/usr/share/doc/graph-tool-2.27/html --with-sysroot=/ --libdir=/usr/lib64 --disable-static --enable-openmp --enable-cairo --with-boost-python=boost_python36 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/lib/portage/python3.7/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking whether make supports nested variables... (cached) yes checking for style of include used by make... GNU checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none checking for library containing strerror... none required checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking dependency style of x86_64-pc-linux-gnu-g++... none checking for x86_64-pc-linux-gnu-gcc option to accept ISO C99... unsupported checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... 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BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for archiver @FILE support... @ checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok checking for sysroot... / checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-pc-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... 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(cached) yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... 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(cached) yes checking whether CGAL is available in /usr... yes checking whether to enable cgal debbuging with valgrind... no checking python3.6 module: numpy... yes checking for numpy/arrayobject.h... yes checking for CAIROMM... yes checking python3.6 module: cairo... yes checking pycairo/py3cairo.h usability... yes checking pycairo/py3cairo.h presence... yes checking for pycairo/py3cairo.h... yes checking whether to enable sparsehash... yes checking for SPARSEHASH... yes checking sparsehash/dense_hash_set usability... yes checking sparsehash/dense_hash_set presence... yes checking for sparsehash/dense_hash_set... yes configure: pkgconfig directory is ${libdir}/pkgconfig checking our pkgconfig libname... graph-tool-py3.6 checking our pkgconfig version... 2.27 checking our pkgconfig_libdir... ${libdir}/pkgconfig expanded our pkgconfig_libdir... /usr/lib64/pkgconfig checking our pkgconfig_libfile... graph-tool-py3.6.pc checking our package / suffix... graph-tool / checking our pkgconfig description... graph-tool Python library checking our pkgconfig requires... checking our pkgconfig ext libs... -L/usr/lib64 -lpython3.6m -lboost_python36 checking our pkgconfig cppflags... -I/usr/lib64/python3.6/site-packages/graph_tool/include -I/usr/lib64/python3.6/site-packages/graph_tool/include/boost-workaround -I/usr/include/python3.6m -pthread -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include checking our pkgconfig ldflags... noninstalled pkgconfig -L /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python3_6/src/.libs noninstalled pkgconfig -I /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python3_6/. checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/graph/Makefile config.status: creating src/graph/centrality/Makefile config.status: creating src/graph/clustering/Makefile config.status: creating src/graph/correlations/Makefile config.status: creating src/graph/draw/Makefile config.status: creating src/graph/flow/Makefile config.status: creating src/graph/generation/Makefile config.status: creating src/graph/inference/Makefile config.status: creating src/graph/layout/Makefile config.status: creating src/graph/search/Makefile config.status: creating src/graph/spectral/Makefile config.status: creating src/graph/stats/Makefile config.status: creating src/graph/topology/Makefile config.status: creating src/graph/util/Makefile config.status: creating src/graph_tool/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands config.status: executing graph-tool-py3.6.pc commands config.status: creating graph-tool-py3.6.pc.in config.status: creating graph-tool-py3.6.pc config.status: creating graph-tool-py3.6-uninstalled.pc config.status: creating graph-tool-py3.6-uninstalled.sh ================================================================================(B  CONFIGURATION SUMMARY (B ================================================================================(B Using python version: 3.6.9(B Python interpreter: /usr/bin/python3.6(B Installation path: /usr/lib64/python3.6/site-packages/graph_tool(B C++ compiler (CXX): x86_64-pc-linux-gnu-g++(B C++ compiler version: 9.2.0(B Prefix: /usr(B Pkgconfigdir: ${libdir}/pkgconfig(B Python CPP flags: -I/usr/include/python3.6m(B Python LD flags: -L/usr/lib64 -lpython3.6m(B Boost CPP flags: -pthread -I/usr/include(B Boost LD flags: -lboost_iostreams-mt -lboost_python36 -lboost_regex-mt -lboost_coroutine-mt(B Numpy CPP flags: -I/usr/lib64/python3.6/site-packages/numpy/core/include(B Sparsehash CPP flags: (B CGAL CPP flags: -I/usr/include(B CGAL LD flags: -L/usr/lib -lCGAL -lCGAL_Core -lgmp -lboost_thread -lpthread(B Expat CPP flags: -I/usr/include(B Expat LD flags: -L/usr/lib -lexpat(B Cairomm CPP flags: -I/usr/include/cairomm-1.0 -I/usr/lib64/cairomm-1.0/include -I/usr/include/cairo -I/usr/lib64/libffi-3.3_rc0/include -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libdrm -I/usr/include/libpng16 -I/usr/include/sigc++-2.0 -I/usr/lib64/sigc++-2.0/include(B Cairomm LD flags: -lcairomm-1.0 -lcairo -lsigc-2.0(B OpenMP compiler flags: -fopenmp(B OpenMP LD flags: (B Extra CPPFLAGS: -DNDEBUG (B Extra CXXFLAGS: -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4(B Extra LDFLAGS: -Wl,-O1 -Wl,--as-needed(B Using OpenMP: yes(B Using sparsehash: yes(B Using cairo: yes(B ================================================================================(B * python3_7: running run_in_build_dir configure * econf: updating graph-tool-2.27-python3_7/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27-python3_7/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.27-python3_6/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27-python3_6/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.27-python2_7/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27-python2_7/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.27/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.27/build-aux/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/graph-tool-2.27 --htmldir=/usr/share/doc/graph-tool-2.27/html --with-sysroot=/ --libdir=/usr/lib64 --disable-static --enable-openmp --enable-cairo --with-boost-python=boost_python37 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/lib/portage/python3.7/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking whether make supports nested variables... (cached) yes checking for style of include used by make... GNU checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none checking for library containing strerror... none required checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking dependency style of x86_64-pc-linux-gnu-g++... none checking for x86_64-pc-linux-gnu-gcc option to accept ISO C99... unsupported checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... 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BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for archiver @FILE support... @ checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok checking for sysroot... / checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-pc-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... 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(cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for x86_64-pc-linux-gnu-pkg-config... /usr/bin/x86_64-pc-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking whether x86_64-pc-linux-gnu-g++ supports C++14 features by default... yes checking whether to enable debug info... no checking whether to enable parallel algorithms with openmp... yes checking for OpenMP flag of C++ compiler... -fopenmp checking whether to enable cairo drawing... yes checking for Expat XML Parser headers in /usr/include... found checking for Expat XML Parser libraries... found checking for Expat XML Parser... yes checking whether /usr/bin/python3.7 version is >= 2.7... yes checking for /usr/bin/python3.7 version... 3.7 checking for /usr/bin/python3.7 platform... linux checking for /usr/bin/python3.7 script directory... ${prefix}/lib/python3.7/site-packages checking for /usr/bin/python3.7 extension module directory... ${exec_prefix}/lib/python3.7/site-packages checking for python3.7... /usr/bin/python3.7 checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '3.7.4'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python3.7m checking for Python library path... -L/usr/lib64 -lpython3.7m checking for Python site-packages path... /usr/lib/python3.7/site-packages checking python extra libraries... -lcrypt -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes checking for boostlib >= 1.55.0 (105500)... yes checking whether the Boost::Python library is available... yes checking whether boost_python37 is the correct library... yes checking whether the Boost::IOStreams library is available... yes checking for exit in -lboost_iostreams-mt... yes checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex-mt... yes checking whether the Boost::Context library is available... no configure: WARNING: No usable boost::context found! Some functionality will be disabled in the library. checking whether the Boost::Coroutine library is available... yes checking for exit in -lboost_coroutine-mt... yes checking whether the Boost::Graph library is available... yes checking for exit in -lboost_graph-mt... yes checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread... yes checking for __gmpz_init in -lgmp... yes checking for __gmpz_init in -lgmp... (cached) yes checking whether CGAL is available in /usr... yes checking whether to enable cgal debbuging with valgrind... no checking python3.7 module: numpy... yes checking for numpy/arrayobject.h... yes checking for CAIROMM... yes checking python3.7 module: cairo... yes checking pycairo/py3cairo.h usability... yes checking pycairo/py3cairo.h presence... yes checking for pycairo/py3cairo.h... yes checking whether to enable sparsehash... yes checking for SPARSEHASH... yes checking sparsehash/dense_hash_set usability... yes checking sparsehash/dense_hash_set presence... yes checking for sparsehash/dense_hash_set... yes configure: pkgconfig directory is ${libdir}/pkgconfig checking our pkgconfig libname... graph-tool-py3.7 checking our pkgconfig version... 2.27 checking our pkgconfig_libdir... ${libdir}/pkgconfig expanded our pkgconfig_libdir... /usr/lib64/pkgconfig checking our pkgconfig_libfile... graph-tool-py3.7.pc checking our package / suffix... graph-tool / checking our pkgconfig description... graph-tool Python library checking our pkgconfig requires... checking our pkgconfig ext libs... -L/usr/lib64 -lpython3.7m -lboost_python37 checking our pkgconfig cppflags... -I/usr/lib/python3.7/site-packages/graph_tool/include -I/usr/lib/python3.7/site-packages/graph_tool/include/boost-workaround -I/usr/include/python3.7m -pthread -I/usr/include -I/usr/lib/python3.7/site-packages/numpy/core/include checking our pkgconfig ldflags... noninstalled pkgconfig -L /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python3_7/src/.libs noninstalled pkgconfig -I /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python3_7/. checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/graph/Makefile config.status: creating src/graph/centrality/Makefile config.status: creating src/graph/clustering/Makefile config.status: creating src/graph/correlations/Makefile config.status: creating src/graph/draw/Makefile config.status: creating src/graph/flow/Makefile config.status: creating src/graph/generation/Makefile config.status: creating src/graph/inference/Makefile config.status: creating src/graph/layout/Makefile config.status: creating src/graph/search/Makefile config.status: creating src/graph/spectral/Makefile config.status: creating src/graph/stats/Makefile config.status: creating src/graph/topology/Makefile config.status: creating src/graph/util/Makefile config.status: creating src/graph_tool/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands config.status: executing graph-tool-py3.7.pc commands config.status: creating graph-tool-py3.7.pc.in config.status: creating graph-tool-py3.7.pc config.status: creating graph-tool-py3.7-uninstalled.pc config.status: creating graph-tool-py3.7-uninstalled.sh ================================================================================(B  CONFIGURATION SUMMARY (B ================================================================================(B Using python version: 3.7.4(B Python interpreter: /usr/bin/python3.7(B Installation path: /usr/lib/python3.7/site-packages/graph_tool(B C++ compiler (CXX): x86_64-pc-linux-gnu-g++(B C++ compiler version: 9.2.0(B Prefix: /usr(B Pkgconfigdir: ${libdir}/pkgconfig(B Python CPP flags: -I/usr/include/python3.7m(B Python LD flags: -L/usr/lib64 -lpython3.7m(B Boost CPP flags: -pthread -I/usr/include(B Boost LD flags: -lboost_iostreams-mt -lboost_python37 -lboost_regex-mt -lboost_coroutine-mt(B Numpy CPP flags: -I/usr/lib/python3.7/site-packages/numpy/core/include(B Sparsehash CPP flags: (B CGAL CPP flags: -I/usr/include(B CGAL LD flags: -L/usr/lib -lCGAL -lCGAL_Core -lgmp -lboost_thread -lpthread(B Expat CPP flags: -I/usr/include(B Expat LD flags: -L/usr/lib -lexpat(B Cairomm CPP flags: -I/usr/include/cairomm-1.0 -I/usr/lib64/cairomm-1.0/include -I/usr/include/cairo -I/usr/lib64/libffi-3.3_rc0/include -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libdrm -I/usr/include/libpng16 -I/usr/include/sigc++-2.0 -I/usr/lib64/sigc++-2.0/include(B Cairomm LD flags: -lcairomm-1.0 -lcairo -lsigc-2.0(B OpenMP compiler flags: -fopenmp(B OpenMP LD flags: (B Extra CPPFLAGS: -DNDEBUG (B Extra CXXFLAGS: -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4(B Extra LDFLAGS: -Wl,-O1 -Wl,--as-needed(B Using OpenMP: yes(B Using sparsehash: yes(B Using cairo: yes(B ================================================================================(B >>> Source configured. >>> Compiling source in /var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27 ... * python2_7: running run_in_build_dir emake -j1 make -j4 -j1 make all-recursive make[1]: Entering directory '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7' Making all in src make[2]: Entering directory '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7/src' Making all in graph make[3]: Entering directory '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7/src/graph' Making all in centrality make[4]: Entering directory '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7/src/graph/centrality' /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall 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-march=native -finline-functions -floop-nest-optimize -flto=4 -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c graph_sbm.cc -fPIC -DPIC -o .libs/graph_sbm.o In file included from /usr/include/python2.7/Python.h:8, from ../../../src/graph/graph.hh:22, from graph_sbm.hh:25, from graph_sbm.cc:18: /usr/include/python2.7/pyconfig.h:1220: warning: "_POSIX_C_SOURCE" redefined 1220 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/c++config.h:524, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/utility:68, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/tuple:38, from graph_sbm.hh:21, from graph_sbm.cc:18: /usr/include/features.h:266: note: this is the location of the previous definition 266 | # define _POSIX_C_SOURCE 200809L | In file included from /usr/include/python2.7/Python.h:8, from ../../../src/graph/graph.hh:22, from graph_sbm.hh:25, from graph_sbm.cc:18: /usr/include/python2.7/pyconfig.h:1242: warning: "_XOPEN_SOURCE" redefined 1242 | #define _XOPEN_SOURCE 600 | In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/c++config.h:524, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/utility:68, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/tuple:38, from graph_sbm.hh:21, from graph_sbm.cc:18: /usr/include/features.h:203: note: this is the location of the previous definition 203 | # define _XOPEN_SOURCE 700 | /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround 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uncertain/.libs/graph_blockmodel_uncertain_marginal.o /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c -o uncertain/graph_blockmodel_uncertain_mcmc.lo uncertain/graph_blockmodel_uncertain_mcmc.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c uncertain/graph_blockmodel_uncertain_mcmc.cc -fPIC -DPIC -o uncertain/.libs/graph_blockmodel_uncertain_mcmc.o /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c -o support/cache.lo support/cache.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c support/cache.cc -fPIC -DPIC -o support/.libs/cache.o /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c -o support/int_part.lo support/int_part.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c support/int_part.cc -fPIC -DPIC -o support/.libs/int_part.o In file included from /usr/include/python2.7/Python.h:8, from ../../../src/graph/graph.hh:22, from ../../../src/graph/graph_tool.hh:21, from support/int_part.cc:21: /usr/include/python2.7/pyconfig.h:1220: warning: "_POSIX_C_SOURCE" redefined 1220 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/c++config.h:524, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/bits/stl_algobase.h:59, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/vector:60, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/zeta.hpp:13, from support/int_part.cc:18: /usr/include/features.h:266: note: this is the location of the previous definition 266 | # define _POSIX_C_SOURCE 200809L | In file included from /usr/include/python2.7/Python.h:8, from ../../../src/graph/graph.hh:22, from ../../../src/graph/graph_tool.hh:21, from support/int_part.cc:21: /usr/include/python2.7/pyconfig.h:1242: warning: "_XOPEN_SOURCE" redefined 1242 | #define _XOPEN_SOURCE 600 | In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/c++config.h:524, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/bits/stl_algobase.h:59, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/vector:60, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/zeta.hpp:13, from support/int_part.cc:18: /usr/include/features.h:203: note: this is the location of the previous definition 203 | # define _XOPEN_SOURCE 700 | /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c -o support/spence.lo support/spence.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c support/spence.cc -fPIC -DPIC -o support/.libs/spence.o /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c -o graph_inference.lo graph_inference.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c graph_inference.cc -fPIC -DPIC -o .libs/graph_inference.o /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c -o graph_modularity.lo graph_modularity.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c graph_modularity.cc -fPIC -DPIC -o .libs/graph_modularity.o In file included from /usr/include/python2.7/Python.h:8, from ../../../src/graph/graph.hh:22, from ../../../src/graph/graph_tool.hh:21, from graph_modularity.hh:26, from graph_modularity.cc:18: /usr/include/python2.7/pyconfig.h:1220: warning: "_POSIX_C_SOURCE" redefined 1220 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/c++config.h:524, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/utility:68, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/tuple:38, from graph_modularity.hh:21, from graph_modularity.cc:18: /usr/include/features.h:266: note: this is the location of the previous definition 266 | # define _POSIX_C_SOURCE 200809L | In file included from /usr/include/python2.7/Python.h:8, from ../../../src/graph/graph.hh:22, from ../../../src/graph/graph_tool.hh:21, from graph_modularity.hh:26, from graph_modularity.cc:18: /usr/include/python2.7/pyconfig.h:1242: warning: "_XOPEN_SOURCE" redefined 1242 | #define _XOPEN_SOURCE 600 | In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/x86_64-pc-linux-gnu/bits/c++config.h:524, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/utility:68, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9/tuple:38, from graph_modularity.hh:21, from graph_modularity.cc:18: /usr/include/features.h:203: note: this is the location of the previous definition 203 | # define _XOPEN_SOURCE 700 | /bin/sh ../../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -module -avoid-version -export-dynamic -no-undefined -Wl,-E -Wl,--as-needed -Wl,-O1 -Wl,--as-needed -o libgraph_tool_inference.la -rpath /usr/lib64/python2.7/site-packages/graph_tool/inference blockmodel/graph_blockmodel.lo blockmodel/graph_blockmodel_em.lo blockmodel/graph_blockmodel_exhaustive.lo blockmodel/graph_blockmodel_gibbs.lo blockmodel/graph_blockmodel_imp.lo blockmodel/graph_blockmodel_imp2.lo blockmodel/graph_blockmodel_imp3.lo blockmodel/graph_blockmodel_marginals.lo blockmodel/graph_blockmodel_mcmc.lo blockmodel/graph_blockmodel_merge.lo blockmodel/graph_blockmodel_multicanonical.lo blockmodel/graph_blockmodel_multicanonical_multiflip.lo blockmodel/graph_blockmodel_multiflip_mcmc.lo overlap/graph_blockmodel_overlap.lo overlap/graph_blockmodel_overlap_exhaustive.lo overlap/graph_blockmodel_overlap_gibbs.lo overlap/graph_blockmodel_overlap_mcmc.lo overlap/graph_blockmodel_overlap_mcmc_bundled.lo overlap/graph_blockmodel_overlap_multicanonical.lo overlap/graph_blockmodel_overlap_multicanonical_multiflip.lo overlap/graph_blockmodel_overlap_multiflip_mcmc.lo overlap/graph_blockmodel_overlap_vacate.lo layers/graph_blockmodel_layers.lo layers/graph_blockmodel_layers_exhaustive.lo layers/graph_blockmodel_layers_gibbs.lo layers/graph_blockmodel_layers_imp.lo 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graph_inference.lo graph_modularity.lo -L/usr/lib64 -lpython2.7 -lboost_iostreams-mt -lboost_python27 -lboost_regex-mt -lboost_coroutine-mt -lexpat -L/usr/lib -lgmp -lgmp libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/crtbeginS.o blockmodel/.libs/graph_blockmodel.o blockmodel/.libs/graph_blockmodel_em.o blockmodel/.libs/graph_blockmodel_exhaustive.o blockmodel/.libs/graph_blockmodel_gibbs.o blockmodel/.libs/graph_blockmodel_imp.o blockmodel/.libs/graph_blockmodel_imp2.o blockmodel/.libs/graph_blockmodel_imp3.o blockmodel/.libs/graph_blockmodel_marginals.o blockmodel/.libs/graph_blockmodel_mcmc.o blockmodel/.libs/graph_blockmodel_merge.o blockmodel/.libs/graph_blockmodel_multicanonical.o blockmodel/.libs/graph_blockmodel_multicanonical_multiflip.o blockmodel/.libs/graph_blockmodel_multiflip_mcmc.o overlap/.libs/graph_blockmodel_overlap.o 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-L/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../lib64/crtn.o -fopenmp -O3 -O2 -march=native -flto=4 -Wl,-E -Wl,--as-needed -Wl,-O1 -Wl,--as-needed -fopenmp -Wl,-soname -Wl,libgraph_tool_inference.so -o .libs/libgraph_tool_inference.so libtool: link: ( cd ".libs" && rm -f "libgraph_tool_inference.la" && ln -s "../libgraph_tool_inference.la" "libgraph_tool_inference.la" ) make[4]: Leaving directory '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7/src/graph/inference' Making all in layout make[4]: Entering directory '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7/src/graph/layout' /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c -o graph_arf.lo graph_arf.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c graph_arf.cc -fPIC -DPIC -o .libs/graph_arf.o /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c -o graph_planar_layout.lo graph_planar_layout.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c graph_planar_layout.cc -fPIC -DPIC -o .libs/graph_planar_layout.o /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c -o graph_fruchterman_reingold.lo graph_fruchterman_reingold.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c graph_fruchterman_reingold.cc -fPIC -DPIC -o .libs/graph_fruchterman_reingold.o /bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c -o graph_sfdp.lo graph_sfdp.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/boost-workaround -DHAVE_CONFIG_H -I../../../src/graph -I../../.. -I/usr/include/python2.7 -pthread -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -DNDEBUG -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -O2 -pipe -march=native -finline-functions -floop-nest-optimize -flto=4 -c graph_sfdp.cc -fPIC -DPIC -o .libs/graph_sfdp.o graph_sfdp.cc: In function ‘void sfdp_layout(graph_tool::GraphInterface&, boost::any, boost::any, boost::any, boost::any, boost::python::api::object, double, double, double, size_t, double, size_t, bool, bool, rng_t&)’: graph_sfdp.cc:55:68: error: call of overloaded ‘any_cast(boost::python::extract)’ is ambiguous 55 | any_cast(python::extract(spring_parms[6])); | ^ In file included from /usr/include/boost/property_map/dynamic_property_map.hpp:24, from ../../../src/graph/graph_properties.hh:34, from ../../../src/graph/graph.hh:35, from ../../../src/graph/graph_filtering.hh:21, from graph_sfdp.cc:18: /usr/include/boost/any.hpp:295:22: note: candidate: ‘ValueType boost::any_cast(const boost::any&) [with ValueType = boost::checked_vector_property_map >]’ 295 | inline ValueType any_cast(const any & operand) | ^~~~~~~~ /usr/include/boost/any.hpp:303:22: note: candidate: ‘ValueType boost::any_cast(boost::any&&) [with ValueType = boost::checked_vector_property_map >]’ 303 | inline ValueType any_cast(any&& operand) | ^~~~~~~~ make[4]: *** [Makefile:530: graph_sfdp.lo] Error 1 make[4]: Leaving directory '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7/src/graph/layout' make[3]: *** [Makefile:752: all-recursive] Error 1 make[3]: Leaving directory '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7/src/graph' make[2]: *** [Makefile:422: all-recursive] Error 1 make[2]: Leaving directory '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7/src' make[1]: *** [Makefile:594: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7' make: *** [Makefile:481: all] Error 2 * ERROR: dev-python/graph-tool-2.27::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=dev-python/graph-tool-2.27::gentoo'`, * the complete build log and the output of `emerge -pqv '=dev-python/graph-tool-2.27::gentoo'`. * The complete build log is located at '/var/gentoo/logs/build/dev-python/graph-tool-2.27:20190924-175026.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/dev-python/graph-tool-2.27/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/dev-python/graph-tool-2.27/temp/environment'. * Working directory: '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27-python2_7' * S: '/var/tmp/portage/dev-python/graph-tool-2.27/work/graph-tool-2.27'