* Package: dev-python/graph-tool-2.35 * Repository: gentoo * Maintainer: python@gentoo.org chr@chymera.eu * USE: abi_x86_64 amd64 cairo elibc_glibc kernel_linux openmp python_targets_python3_6 python_targets_python3_7 python_targets_python3_8 python_targets_python3_9 userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox @@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; This ebuild was merged at the following commit: https://github.com/gentoo-mirror/gentoo/commit/6c97912ec9ece621b9656d9ef304e26790252e13 (Mon Oct 12 18:35:14 UTC 2020) @@@@@ END @@@@@ emerge --info: Portage 3.0.8 (python 3.8.6-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r2, 5.4.0-1025-aws x86_64) ================================================================= System uname: Linux-5.4.0-1025-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8175M_CPU_@_2.50GHz-with-glibc2.2.5 KiB Mem: 64359964 total, 21838784 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Mon, 12 Oct 2020 18:35:13 +0000 sh bash 5.0_p18 ld GNU ld (Gentoo 2.35.1 p1) 2.35.1 app-shells/bash: 5.0_p18::gentoo dev-lang/perl: 5.30.3-r1::gentoo dev-lang/python: 2.7.18-r4::gentoo, 3.6.12::gentoo, 3.7.9::gentoo, 3.8.6::gentoo, 3.9.0::gentoo dev-util/cmake: 3.18.4::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.20::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.16.2::gentoo sys-devel/binutils: 2.35.1::gentoo sys-devel/gcc: 10.2.0-r2::gentoo sys-devel/gcc-config: 2.3.2::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.8::gentoo (virtual/os-headers) sys-libs/glibc: 2.32-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* GPL-3" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" DISTDIR="/var/tmp/portage/dev-python/graph-tool-2.35/distdir" EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -b -k" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="C.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=gold" MAKEOPTS="-j16 V=1" PKGDIR="/root/.packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 berkdb bzip2 cairo cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" PYTHON_TARGETS="python3_6 python3_7 python3_8 python3_9" USERLAND="GNU" Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS >>> Unpacking source... >>> Unpacking graph-tool-2.35.tar.bz2 to /var/tmp/portage/dev-python/graph-tool-2.35/work >>> Source unpacked in /var/tmp/portage/dev-python/graph-tool-2.35/work >>> Preparing source in /var/tmp/portage/dev-python/graph-tool-2.35/work/graph-tool-2.35 ... * Will copy sources from /var/tmp/portage/dev-python/graph-tool-2.35/work/graph-tool-2.35 * python3_6: copying to /var/tmp/portage/dev-python/graph-tool-2.35/work/graph-tool-2.35-python3_6 * python3_7: copying to /var/tmp/portage/dev-python/graph-tool-2.35/work/graph-tool-2.35-python3_7 * python3_8: copying to /var/tmp/portage/dev-python/graph-tool-2.35/work/graph-tool-2.35-python3_8 * python3_9: copying to /var/tmp/portage/dev-python/graph-tool-2.35/work/graph-tool-2.35-python3_9 >>> Source prepared. >>> Configuring source in /var/tmp/portage/dev-python/graph-tool-2.35/work/graph-tool-2.35 ... * python3_6: running run_in_build_dir configure * econf: updating graph-tool-2.35-python3_6/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.35-python3_6/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.35-python3_8/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.35-python3_8/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.35-python3_7/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.35-python3_7/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.35-python3_9/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.35-python3_9/build-aux/config.guess with /usr/share/gnuconfig/config.guess * econf: updating graph-tool-2.35/build-aux/config.sub with /usr/share/gnuconfig/config.sub * econf: updating graph-tool-2.35/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-2.35 --htmldir=/usr/share/doc/graph-tool-2.35/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/python3.8/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 whether make supports the include directive... yes (GNU style) 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... (cached) none needed checking for x86_64-pc-linux-gnu-gcc option to accept ISO Standard C... (cached) none needed checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for ANSI C header files... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-ld.gold checking if the linker (x86_64-pc-linux-gnu-ld.gold) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... 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 x86_64-pc-linux-gnu-ld.gold 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++17 features by default... no checking whether x86_64-pc-linux-gnu-g++ supports C++17 features with -std=gnu++17... yes configure: WARNING: C++17 is not yet standardized, so the checks may change in incompatible ways anytime 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... yes checking whether /usr/bin/python3.6 version is >= 2.7... yes checking for /usr/bin/python3.6 version... 3.6 checking for /usr/bin/python3.6 platform... linux checking for /usr/bin/python3.6 script directory... ${prefix}/lib64/python3.6/site-packages checking for /usr/bin/python3.6 extension module directory... ${exec_prefix}/lib64/python3.6/site-packages checking for python3.6... /usr/bin/python3.6 checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '3.6.12'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python3.6m checking for Python library path... -L/usr/lib64 -lpython3.6m checking for Python site-packages path... /usr/lib64/python3.6/site-packages checking python extra libraries... -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_python36 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... yes checking for exit in -lboost_context-mt... yes 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 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... no Traceback (most recent call last): File "", line 1, in File "/usr/lib64/python3.6/site-packages/cairo/__init__.py", line 1, in from ._cairo import * # noqa: F401,F403 ImportError: /usr/lib64/python3.6/site-packages/cairo/_cairo.cpython-36m-x86_64-linux-gnu.so: undefined symbol: cairo_xlib_surface_get_width checking py3cairo.h usability... no checking py3cairo.h presence... no checking for py3cairo.h... no configure: error: pycairo headers not found !!! Please attach the following file when seeking support: !!! /var/tmp/portage/dev-python/graph-tool-2.35/work/graph-tool-2.35-python3_6/config.log * ERROR: dev-python/graph-tool-2.35::gentoo failed (configure phase): * econf failed * * Call stack: * ebuild.sh, line 125: Called src_configure * environment, line 2585: Called python_foreach_impl 'run_in_build_dir' 'configure' * environment, line 2206: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'run_in_build_dir' 'configure' * environment, line 1641: Called _multibuild_run '_python_multibuild_wrapper' 'run_in_build_dir' 'configure' * environment, line 1639: Called _python_multibuild_wrapper 'run_in_build_dir' 'configure' * environment, line 679: Called run_in_build_dir 'configure' * environment, line 2570: Called configure * environment, line 2583: Called econf '--disable-static' '--enable-openmp' '--enable-cairo' '--with-boost-python=boost_python36' * phase-helpers.sh, line 681: Called __helpers_die 'econf failed' * isolated-functions.sh, line 112: Called die * The specific snippet of code: * die "$@" * * If you need support, post the output of `emerge --info '=dev-python/graph-tool-2.35::gentoo'`, * the complete build log and the output of `emerge -pqv '=dev-python/graph-tool-2.35::gentoo'`. * The complete build log is located at '/var/log/emerge-log/build/dev-python/graph-tool-2.35:20201012-191249.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/dev-python/graph-tool-2.35/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/dev-python/graph-tool-2.35/temp/environment'. * Working directory: '/var/tmp/portage/dev-python/graph-tool-2.35/work/graph-tool-2.35-python3_6' * S: '/var/tmp/portage/dev-python/graph-tool-2.35/work/graph-tool-2.35'