This happens with gcc-4.3.6 and 4.5.3 at least. conv_template:> build-3.1/src.linux-x86_64-3.1/numpy/core/src/_sortmodule.c numpy.core - nothing done with h_files = ['build-3.1/src.linux-x86_64-3.1/numpy/core/include/numpy/config.h', 'build-3.1/src.linux-x86_64-3.1/numpy/core/include/numpy/_numpyconfig.h', 'build-3.1/src.linux-x86_64-3.1/numpy/core/include/numpy/__multiarray_api.h'] building extension "numpy.core.multiarray" sources non-existing path in 'numpy/core': 'build-3.1/src.linux-x86_64-3.1/numpy/core/src/multiarray' creating build-3.1/src.linux-x86_64-3.1/numpy/core/src/multiarray conv_template:> build-3.1/src.linux-x86_64-3.1/numpy/core/src/multiarray/scalartypes.c conv_template:> build-3.1/src.linux-x86_64-3.1/numpy/core/src/multiarray/arraytypes.c conv_template:> build-3.1/src.linux-x86_64-3.1/numpy/core/src/multiarray/nditer.c conv_template:> build-3.1/src.linux-x86_64-3.1/numpy/core/src/multiarray/lowlevel_strided_loops.c /var/tmp/portage/dev-python/numpy-1.6.2/temp/environment: line 1327: 28559 Segmentation fault (core dumped) "$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build -b "$(_distutils_get_build_dir)" "$@" * ERROR: dev-python/numpy-1.6.2 failed (compile phase): * Building failed with CPython 3.1 in distutils_building() function * * Call stack: * ebuild.sh, line 85: Called src_compile # emerge --info =dev-python/numpy-1.6.2 Portage 2.1.10.56 (default/linux/amd64/10.0, gcc-4.5.3, glibc-2.15-r2, 3.4.0-rc7-default x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.4.0-rc7-default-x86_64-Intel-R-_Core-TM-_i7-2640M_CPU_@_2.80GHz-with-gentoo-2.1 Timestamp of tree: Wed, 30 May 2012 12:00:01 +0000 app-shells/bash: 4.2_p28 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.5.4-r4, 2.6.8, 2.7.3-r2, 3.1.5, 3.2.3-r1 dev-util/cmake: 2.8.8-r2 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1-r1 sys-apps/openrc: 0.9.9.3 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.11.5 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.2.4-r1, 4.3.6-r1, 4.5.3-r2 sys-devel/gcc-config: 1.7.1 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 3.4 (virtual/os-headers) sys-libs/glibc: 2.15-r2 Repositories: gentoo gentoo-haskell science x-portage x-layman ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE skype-eula Nero-EULA-US AdobeFlash-10.3" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe -march=native" DISTDIR="/mnt/external/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en cs cz" MAKEOPTS="-j8" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/mnt/external/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/haskell /home/mmokrejs/proj/sci /usr/local/portage /var/lib/layman" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X acl acpi alsa amd64 amr apache apache2 berkdb bluetooth bzip2 cairo cgi cli consolekit cracklib crypt cups cxx dbus device-mapper dhcp dri emboss encode fax ffmpeg flac fontconfig fortran gd gdbm gimp gpm gtk gudev hal hpijs iconv id3tag innodb java jce jpeg jpg ladspa laptop lcms libnotify lm_sensors mad mmx modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly nsplugin ntfsprogs ocr ogg opengl openmp openssl pam parport pcre pdf perl php png policykit ppds pppd python readline resolvconf scanner server session sndfile sqlite sse sse2 sse3 ssl suexec svg syslog tcpd threads tiff tk truetype udev unicode usb wavpack xml xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en cs cz" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="vesa intel i915 vmware fbdev" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON # emerge -pqv =dev-python/numpy-1.6.2 [ebuild U ] dev-python/numpy-1.6.2 [1.6.1-r1] USE="-doc -lapack -test"
Created attachment 313601 [details] build.log
Here is the part of environment file with line numbers shown: 1314 distutils_src_compile () 1315 { 1316 if [[ "${EBUILD_PHASE}" != "compile" ]]; then 1317 die "${FUNCNAME}() can be used only in src_compile() phase"; 1318 fi; 1319 _python_check_python_pkg_setup_execution; 1320 _python_set_color_variables; 1321 local setup_file; 1322 if _python_package_supporting_installation_for_multiple_python_abis; then 1323 function distutils_building () 1324 { 1325 _distutils_hook pre; 1326 _distutils_prepare_global_options; 1327 for setup_file in "${DISTUTILS_SETUP_FILES[@]-setup.py}"; 1328 do 1329 _distutils_prepare_current_working_directory "${setup_file}"; 1330 echo ${_BOLD}"$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build -b "$(_distutils_get_build_dir)" "$@"${_NORMAL}; 1331 "$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build -b "$(_distutils_get_build_dir)" "$@" || return "$?"; 1332 _distutils_restore_current_working_directory "${setup_file}"; 1333 done; 1334 _distutils_hook post 1335 }; 1336 python_execute_function ${DISTUTILS_USE_SEPARATE_SOURCE_DIRECTORIES:+-s} distutils_building "$@"; 1337 unset -f distutils_building; 1338 else 1339 _distutils_prepare_global_options; 1340 for setup_file in "${DISTUTILS_SETUP_FILES[@]-setup.py}"; 1341 do 1342 _distutils_prepare_current_working_directory "${setup_file}"; 1343 echo ${_BOLD}"$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build "$@"${_NORMAL}; 1344 "$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build "$@" || die "Building failed"; 1345 _distutils_restore_current_working_directory "${setup_file}"; 1346 done; 1347 fi 1348 } "revdep-rebuild -i" does not report any issues, I am running now python-updater to make sure that is not an issue: # python-updater * Starting Python Updater... * Main active version of Python: 2.7 * Active version of Python 2: 2.7 * Active version of Python 3: 3.1 * Globally supported Python ABIs in installed repositories: * gentoo: 2.4 2.5 2.6 2.7 3.1 3.2 2.5-jython 2.7-pypy-1.7 2.7-pypy-1.8 * gentoo-haskell: 2.4 2.5 2.6 2.7 3.1 3.2 2.5-jython 2.7-pypy-1.7 2.7-pypy-1.8 * science: 2.4 2.5 2.6 2.7 3.1 3.2 2.5-jython 2.7-pypy-1.7 2.7-pypy-1.8 * x-layman: 2.4 2.5 2.6 2.7 3.1 3.2 2.5-jython 2.7-pypy-1.7 2.7-pypy-1.8 * x-portage: 2.4 2.5 2.6 2.7 3.1 3.2 2.5-jython 2.7-pypy-1.7 2.7-pypy-1.8
Is this still reproducable?
I cannot reproduce it anymore with any of gcc 4.6.3, 4.5.3, 4.3.6 and # emerge -pv =dev-python/numpy-1.6.2 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] dev-python/numpy-1.6.2 USE="-doc -lapack {-test}" 0 kB # I am puzzled. # emerge --info =dev-python/numpy-1.6.2 Portage 2.1.11.33 (default/linux/amd64/10.0, gcc-4.3.6, glibc-2.16.0, 3.4.17-default x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.4.17-default-x86_64-Intel-R-_Core-TM-_i7-2640M_CPU_@_2.80GHz-with-gentoo-2.2 Timestamp of tree: Fri, 07 Dec 2012 09:30:01 +0000 ld GNU ld (GNU Binutils) 2.23.1 app-shells/bash: 4.2_p39 dev-java/java-config: 2.1.12 dev-lang/python: 2.5.4-r4, 2.6.8, 2.7.3-r2, 3.2.3-r1 dev-util/cmake: 2.8.9-r1 dev-util/pkgconfig: 0.27.1 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.6 sys-apps/sandbox: 2.6 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.11.6, 1.12.5 sys-devel/binutils: 2.23.1 sys-devel/gcc: 4.2.4-r1, 4.3.6-r1, 4.5.3-r2, 4.6.3 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.6 (virtual/os-headers) sys-libs/glibc: 2.16.0 Repositories: gentoo gentoo-haskell science x-portage x-layman ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4 -mavx -maes -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa" CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4 -mavx -maes -march=native" DISTDIR="/mnt/external/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/mnt/external/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/haskell /home/mmokrejs/proj/sci /usr/local/portage /var/lib/layman" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X acl acpi alsa amd64 amr apache apache2 berkdb bluetooth bzip2 cairo cgi cli cracklib crypt cups cxx dbus device-mapper dhcp dri emboss encode fax ffmpeg flac fontconfig fortran gd gdbm gimp gpm gtk gudev hal hpijs hwdb iconv id3tag innodb java jce jpeg jpg keymap ladspa laptop lcms libnotify lm_sensors mad mmx modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly nsplugin ntfsprogs ocr ogg opengl openmp openssl pam parport pcre pdf perl php png policykit ppds pppd python readline resolvconf scanner server session sndfile sqlite sse sse2 sse3 ssl suexec svg syslog tcpd threads tiff tk truetype udev unicode usb vim-syntax wavpack x11 xml xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en cs cz" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="vesa vmware fbdev intel i915 i965 nouveau" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= dev-python/numpy-1.6.2 was built with the following: USE="(multilib) -doc -lapack -test" CFLAGS="-O2 -pipe -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4 -march=native" LDFLAGS="-Wl,-O1 -Wl,--as-needed -shared"
The original report was with python 3.1 you have now moved to python 3.2, It may be why things are looking up now.
