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Bug 380597 - sci-libs/scipy-0.9.0-r1 fails to emerge due to missing blas and atlas libraries
Summary: sci-libs/scipy-0.9.0-r1 fails to emerge due to missing blas and atlas libraries
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Library (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
Depends on:
Reported: 2011-08-25 07:47 UTC by Juergen Rose
Modified: 2012-12-07 07:40 UTC (History)
0 users

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

/var/tmp/portage/sci-libs/scipy-0.9.0-r1/temp/build.log (build.log,510.28 KB, text/plain)
2011-08-25 07:48 UTC, Juergen Rose

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Description Juergen Rose 2011-08-25 07:47:22 UTC
'emerge scipy' fails with:
RefactoringTool: /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/sparse/linalg/dsolve/umfpack/
RefactoringTool: /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/sparse/linalg/isolve/
RefactoringTool: /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/
  libraries mkl,vml,guide not found in /usr/local/lib64
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib64
  libraries mkl,vml,guide not found in /usr/lib

Warning: No configuration returned, assuming unavailable./usr/lib64/python3.2/site-packages/numpy/distutils/ UserWarning: Specified path  is invalid.
  warnings.warn('Specified path %s is invalid.' % d)
  libraries atlcblas,f77blas,m,atlas not found in /usr/lib64

  libraries atlcblas,f77blas,m,atlas not found in /usr/lib64

/usr/lib64/python3.2/site-packages/numpy/distutils/ UserWarning: 
    Atlas ( libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  libraries blas not found in /usr/local/lib64
  libraries blas not found in /usr/local/lib
  libraries blas not found in /usr/lib64
  libraries blas not found in /usr/lib

/usr/lib64/python3.2/site-packages/numpy/distutils/ UserWarning: 
    Blas ( libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [blas]) or by setting
    the BLAS environment variable.

/usr/lib64/python3.2/site-packages/numpy/distutils/ UserWarning: 
    Blas ( sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [blas_src]) or by setting
    the BLAS_SRC environment variable.
Traceback (most recent call last):
  File "", line 181, in <module>
  File "", line 173, in setup_package
    configuration=configuration )
  File "/usr/lib64/python3.2/site-packages/numpy/distutils/", line 310, in get_info
    return cl().get_info(notfound_action)
  File "/usr/lib64/python3.2/site-packages/numpy/distutils/", line 461, in get_info
    raise self.notfounderror(self.notfounderror.__doc__)
    Blas ( libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [blas]) or by setting
    the BLAS environment variable.
 * ERROR: sci-libs/scipy-0.9.0-r1 failed (compile phase):
 *   Building failed with CPython 3.2 in distutils_building() function

I could intall scipy-0.9.0-r1 in the last months. Then I downgraded numpy to numpy-1.5.1 for sage and Bug 371099. After the deletion scipy the next installation of scipy failed.

Reproducible: Always

root@caiman:/root(72)# emerge --info =sci-libs/scipy-0.9.0-r1
Portage (default/linux/amd64/10.0, gcc-4.5.3, glibc-2.13-r4, 3.0.3-gentoo x86_64)
                        System Settings
System uname: Linux-3.0.3-gentoo-x86_64-AMD_Phenom-tm-_II_X6_1090T_Processor-with-gentoo-2.0.3
Timestamp of tree: Wed, 24 Aug 2011 10:00:01 +0000
app-shells/bash:          4.2_p10
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r2::sage-on-gentoo, 3.2-r2
dev-util/cmake:           2.8.5-r2
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.8.3-r1
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.1-r1
sys-devel/binutils:       2.21.1-r1
sys-devel/gcc:            4.5.3-r1
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 2.6.39 (virtual/os-headers)
sys-libs/glibc:           2.13-r4
Repositories: gentoo sunrise x11 bicatali java-overlay science sage-on-gentoo x-portage x-cpan x-g-octave
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft"
CFLAGS="-march=amdfam10 -O2 -pipe"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/ext-active/ /etc/php/cli-php5.3/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=amdfam10 -O2 -pipe"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTDIR_OVERLAY="/var/lib/layman/sunrise /var/lib/layman/x11 /var/lib/layman/bicatali /var/lib/layman/java-overlay /var/lib/layman/science /var/lib/layman/sage-on-gentoo /usr/local/portage /var/lib/cpan /var/lib/g-octave"
USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 amrr ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib crypt css cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pam pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4a ssl stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales utempter v4l2 vaapi video virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets xattr xcb xemacs xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" 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 auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan 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" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="radeon vesa" 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"

                        Package Settings

sci-libs/scipy-0.9.0-r1 was built with the following:
USE="doc (multilib) -umfpack"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -shared"

root@caiman:/root(73)# emerge -pqv =sci-libs/scipy-0.9.0-r1
[ebuild   R   ] sci-libs/scipy-0.9.0-r1  USE="doc -umfpack"
Comment 1 Juergen Rose 2011-08-25 07:48:58 UTC
Created attachment 284557 [details]
Comment 2 Juergen Rose 2011-08-25 07:51:08 UTC
BTW. sci-libs/atlas-3.9.47 is installed:

root@caiman:/root(78)# ll /usr/lib/libblas*
-rw-r--r-- 1 root root 750292 Jan 25  2011 /usr/lib/libblast.a
-rw-r--r-- 1 root root 174668 Jan 25  2011 /usr/lib/libblastapi.a
-rw-r--r-- 1 root root 102396 Jan 25  2011 /usr/lib/libblastcompadj.a
root@caiman:/root(79)# qlist -Iv atlas
Comment 3 daniel 2012-03-02 13:37:07 UTC
I can confirmed this bug.

A solution for me was:

  emerge sci-libs/clapack sci-libs/lapack-atlas
  eselect blas set atlas
  eselect cblas set atlas
  eselect lapack set atlas
  emerge sci-libs/scipy
Comment 4 Andrea Arteaga (RETIRED) gentoo-dev 2012-03-25 00:37:17 UTC
Upgrading numpy and emerging scipy-0.10 could be a solution. See bug 404435.
Comment 5 Justin Lecher (RETIRED) gentoo-dev 2012-12-04 09:56:51 UTC
Still present for latest versions of blas/lapack from sci overlay?