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Gentoo's Bugzilla – Attachment 664975 Details for
Bug 748252
dev-python/graph-tool-2.35 fails to compile
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build.log
build.log (text/plain), 18.14 KB, created by
Agostino Sarubbo
on 2020-10-13 06:56:49 UTC
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-10-13 06:56:49 UTC
Size:
18.14 KB
patch
obsolete
> * 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... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc linker (x86_64-pc-linux-gnu-ld.gold -m elf_x86_64) supports shared libraries... yes >checking whether -lc should be explicitly linked in... no >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether stripping libraries is possible... yes >checking if libtool supports shared libraries... yes >checking whether to build shared libraries... yes >checking whether to build static libraries... no >checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E >checking for ld used by x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-ld.gold -m elf_x86_64 >checking if the linker (x86_64-pc-linux-gnu-ld.gold -m elf_x86_64) is GNU ld... yes >checking whether the x86_64-pc-linux-gnu-g++ linker (x86_64-pc-linux-gnu-ld.gold -m elf_x86_64) supports shared libraries... yes >checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-g++ linker (x86_64-pc-linux-gnu-ld.gold -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... (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 "<string>", line 1, in <module> > File "/usr/lib64/python3.6/site-packages/cairo/__init__.py", line 1, in <module> > 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'
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