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Bug 444104 - sci-libs/scipy-0.11.0 - numpy.distutils.system_info.BlasNotFoundError
Summary: sci-libs/scipy-0.11.0 - numpy.distutils.system_info.BlasNotFoundError
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
Depends on:
Reported: 2012-11-20 21:45 UTC by Antoine Lemoine
Modified: 2013-08-27 18:33 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---

build.log (build.log,6.20 KB, text/plain)
2012-11-20 21:46 UTC, Antoine Lemoine
/var/tmp/portage/sci-libs/scipy-0.11.0/work/scipy-0.11.0/site.cfg (file_444104.txt,279 bytes, text/plain)
2012-11-28 09:42 UTC, Antoine Lemoine
scipy buid log (build.log,6.16 KB, text/plain)
2012-12-05 17:21 UTC, urcindalo

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Description Antoine Lemoine 2012-11-20 21:45:51 UTC
sci-libs/scipy-0.11.0 does not found blas libraries

Versions available are:

# eselect blas list
Available providers for blas:
  [1]   mkl32-dynamic
  [2]   mkl32-dynamic-openmp
  [3]   mkl32-gfortran
  [4]   mkl32-gfortran-openmp
  [5]   mkl32-intel
  [6]   mkl32-intel-openmp
  [7]   mkl64-dynamic
  [8]   mkl64-dynamic-openmp
  [9]   mkl64-gfortran
  [10]  mkl64-gfortran-openmp
  [11]  mkl64-int64-dynamic
  [12]  mkl64-int64-dynamic-openmp
  [13]  mkl64-int64-gfortran
  [14]  mkl64-int64-gfortran-openmp
  [15]  mkl64-int64-intel
  [16]  mkl64-int64-intel-openmp
  [17]  mkl64-intel
  [18]  mkl64-intel-openmp

None of them allows to emerge scipy

Reproducible: Always

Portage (default/linux/amd64/10.0/desktop/gnome, gcc-4.7.2, glibc-2.16.0, 3.6.6-gentoo x86_64)
                         System Settings
System uname: Linux-3.6.6-gentoo-x86_64-Intel-R-_Core-TM-_i7-3770K_CPU_@_3.50GHz-with-gentoo-2.2
Timestamp of tree: Tue, 20 Nov 2012 18:45:01 +0000
ld GNU ld (GNU Binutils) 2.23.1
ccache version 3.1.8 [enabled]
app-shells/bash:          4.2_p39
dev-java/java-config:     2.1.12
dev-lang/python:          2.7.3-r2, 3.2.3-r1
dev-util/ccache:          3.1.8
dev-util/pkgconfig:       0.27.1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.5
sys-apps/sandbox:         2.6
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.6, 1.12.5
sys-devel/binutils:       2.23.1
sys-devel/gcc:            4.7.2
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 science steam-overlay local
ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-march=native -O2 -pipe -floop-interchange -floop-strip-mine -floop-block"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
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="-march=native -O2 -pipe -floop-interchange -floop-strip-mine -floop-block"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs candy ccache config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
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"
PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/steam-overlay /usr/local/portage"
USE="X a52 aac acl acpi alsa amd64 avx bash-completion berkdb boost branding bzip2 cairo cdda cdr cleartype cli colord consolekit corefonts cracklib crypt ctype cxx dbus djvu dri dts dvd dvdr emboss encode evo examples exif fam ffmpeg firefox flac fortran gdbm gif gnome gnome-keyring gnome-online-accounts gpm graphite gstreamer gtk iconv icu ipv6 jpeg jpeg2k lcms ldap libnotify lm_sensors mad mmx mng modules mp3 mp4 mpeg mudflap multilib mysql nautilus ncurses nls nptl ntfs nvidia objc objc++ objc-gc ogg opengl openmp pam pango pcre pdf php plugins png policykit ppds pppd pulseaudio qt3support qt4 quicktime readline remote sasl sdl session socialweb spell sse sse2 sse3 sse4 sse4_1 ssl ssse3 startup-notification svg symlink tcpd threads tiff truetype udev udisks unicode upnp upower usb v4l vim-syntax vorbis wxwidgets x264 xcb xml xv xvid xvmc 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="fr" PHP_TARGETS="php5-4" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nvidia intel" 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"
Comment 1 Antoine Lemoine 2012-11-20 21:46:34 UTC
Created attachment 330100 [details]
Comment 2 Antoine Lemoine 2012-11-28 09:15:54 UTC
sci-libs/scipy-0.11.0 emerges fine when I use sci-libs/blas-reference.
Comment 3 François Bissey 2012-11-28 09:29:56 UTC
Could you post the matching
that goes with the log failure?
Comment 4 Antoine Lemoine 2012-11-28 09:42:59 UTC
Created attachment 330813 [details]
Comment 5 urcindalo 2012-12-05 17:21:06 UTC
Created attachment 331556 [details]
scipy buid log

Same here. I can't reinstall scipy since I installed sci-libs/mkl- from the science overlay. I attach the build.log.
Just in case, I also installed dev-lang/icc- and dev-lang/ifc- from the science overlay.

This is the content of my site.cfg file:
include_dirs = /opt/intel/composerxe-2013.0.079/mkl/include  
library_dirs = /opt/intel/composerxe-2013.0.079/mkl/lib/intel64  :/usr/lib64
blas_libs = mkl_intel_lp64kl_sequentialkl_corekl_rt
library_dirs = /opt/intel/composerxe-2013.0.079/mkl/lib/intel64  :/usr/lib64
lapack_libs = mkl_rt

And these are my blas and lapack eselections:
$ sudo eselect lapack list                                                                                    
Available providers for lapack:
  [7]   mkl64-dynamic *
$ sudo eselect blas list
  [7]   mkl64-dynamic *
Comment 6 Justin Lecher (RETIRED) gentoo-dev 2012-12-06 15:49:39 UTC
Perhaps you could use the reference implementations. They work fine.
Comment 7 Sébastien Fabbro (RETIRED) gentoo-dev 2013-08-27 18:33:29 UTC
+  27 Aug 2013; Sébastien Fabbro <>
+  +files/numpy-1.7.1-distutils-python33.patch, -numpy-1.7.0.ebuild,
+  numpy-1.7.1.ebuild:
+  Remove trailing spaces from pkg-config calls (bug #444104), fix shared lib
+  extension (upstream patch) for python-3 (bug #470946), remove old

+  27 Aug 2013; Sébastien Fabbro <> scipy-0.12.0.ebuild:
+  Remove trailing spaces from pkg-config calls (bug #444104)