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Bug 317121 - sci-libs/scipy-0.7.2 fails to emerge
Summary: sci-libs/scipy-0.7.2 fails to emerge
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Gentoo Science Related Packages
Depends on:
Reported: 2010-04-25 13:35 UTC by Benjamin Schulz
Modified: 2010-04-27 17:12 UTC (History)
0 users

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


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Description Benjamin Schulz 2010-04-25 13:35:48 UTC
emerge scipi leads to

>>> Preparing source in /tmp/portage/sci-libs/scipy-0.7.2/work/scipy-0.7.2 ...
 * Applying scipy-0.7.0_beta1-implicit.patch ...                                                                                                [ ok ]
 * Applying scipy-0.6.0-stsci.patch ...                                                                                                         [ ok ]
 * Applying scipy-0.7.1-weave.patch ...                                                                                                         [ ok ]
>>> Source prepared.
>>> Configuring source in /tmp/portage/sci-libs/scipy-0.7.2/work/scipy-0.7.2 ...
>>> Source configured.
>>> Compiling source in /tmp/portage/sci-libs/scipy-0.7.2/work/scipy-0.7.2 ...
 * Building of sci-libs/scipy-0.7.2 with CPython 2.6...
python2.6 build -b build-2.6 config_fc --noopt --noarch
Traceback (most recent call last):
  File "", line 160, in <module>
  File "", line 127, in setup_package
    from numpy.distutils.core import setup
  File "/usr/lib64/python2.6/site-packages/numpy/", line 132, in <module>
    import add_newdocs
  File "/usr/lib64/python2.6/site-packages/numpy/", line 9, in <module>
    from lib import add_newdoc
  File "/usr/lib64/python2.6/site-packages/numpy/lib/", line 13, in <module>
    from polynomial import *
  File "/usr/lib64/python2.6/site-packages/numpy/lib/", line 17, in <module>
    from numpy.linalg import eigvals, lstsq
  File "/usr/lib64/python2.6/site-packages/numpy/linalg/", line 47, in <module>
    from linalg import *
  File "/usr/lib64/python2.6/site-packages/numpy/linalg/", line 22, in <module>
    from numpy.linalg import lapack_lite
ImportError: /usr/lib/ undefined symbol: clapack_ilaenv
 * ERROR: sci-libs/scipy-0.7.2 failed:
 *   Building failed with CPython 2.6 in distutils_building() function
 * Call stack:
 *, line   54:  Called src_compile
 *   environment, line 5032:  Called distutils_src_compile 'config_fc' '--noopt' '--noarch'
 *   environment, line 1392:  Called python_execute_function 'distutils_building' 'config_fc' '--noopt' '--noarch'
 *   environment, line 3782:  Called die
 * The specific snippet of code:
 *                       die "${failure_message}";
 * If you need support, post the output of 'emerge --info =sci-libs/scipy-0.7.2',
 * the complete build log and the output of 'emerge -pqv =sci-libs/scipy-0.7.2'.
 * The complete build log is located at '/tmp/portage/sci-libs/scipy-0.7.2/temp/build.log'.
 * The ebuild environment file is located at '/tmp/portage/sci-libs/scipy-0.7.2/temp/environment'.
 * S: '/tmp/portage/sci-libs/scipy-0.7.2/work/scipy-0.7.2'

Reproducible: Always

emerge --info
Portage (default/linux/amd64/10.0, gcc-4.4.3, glibc-2.11-r1, 2.6.33-gentoo x86_64)
System uname: Linux-2.6.33-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T9300_@_2.50GHz-with-gentoo-2.0.1
Timestamp of tree: Sun, 25 Apr 2010 12:30:01 +0000
app-shells/bash:     4.1_p5
dev-java/java-config: 2.1.10
dev-lang/python:     2.6.5-r1, 3.1.2-r2
dev-util/cmake:      2.8.1-r1
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.6.1-r1
sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.13, 2.65
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1
sys-devel/gcc:       4.3.4, 4.4.3
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.33
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA dlj-1.1 ut2003 sun-bcla-java-vm"
CFLAGS="-march=native -O2 -pipe -fomit-frame-pointer"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/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 -fomit-frame-pointer"
FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans"
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="/usr/layman/layman/xwing /usr/layman/layman/wschlich-testing /usr/layman/layman/kde /usr/layman/layman/sunrise /usr/layman/layman/qting-edge /usr/layman/layman/science /usr/layman/ownebuilds"
USE="64bit X Xaw3d a52 aac abiword abyss ace acl acpi activefilter addns addressbook admin adns adplug aften afterimage aim aio akonadi alsa amd64 amr amrnb analogtv animgif archive aspell assistant audacious audio audiofile audioscrobbler auth auto-completion automount autoreplace autotrace bash-completion battery bcmath berkdb binary-drivers bittorrent blender blender-game bluetooth bonjour boost browser bugzilla bzip2 cairo calendar caps cardbus ccache cdb cddax cddb cdio cdparanoia cdr cdrom cg cgi chroot cli clipboard cluster cmake compat compress connection-sharing consolekit context contrast contrast-control contrib corefonts cpudetection cpulimit cracklib crypt ctype ctypes-python cuda cue cups cvs cxx cyrillic dbus dc1394 dcc dchroot deflate detex devfs-compat device-mapper dga dia dirac disk-partition diskio dmraid dmx docbook dolby-record-switch dolbyinrec dot dpms drawing dri dts dv dvb dvbplayer dvbsetup dvd dvdarchive dvdchapjump dvdnav dvdr dvi dvi2tty dvipdfm dx dxr3 dynamicplugin ebook eclipse emacs emovix enca enchant encode ethernet ewf excel exif extensions extra extra-algorithms extras faad facebook fame fasttrack fat ffmpeg fftw filter firefox firefox3 fits flac flash flatfile fluidsynth flv fontconfig foomaticdb fortran fortran95 fpx freemail ftp fts3 gadu gallium games gd gdbm gfortran ggi gif git github glib glibc-compat20 glibc-omitfp glsl glut glviewer gmm gmp gmtfull gmthigh gmtsuppl gnome-print gnomecanvas gnuplot gnutella gnutls google google-gadgets gphoto2 gpm grace grammar graph graphics graphite graphviz grass groupwise grub gs gsf gsl gsm gstreamer gtk gtk2-perl gtkhotkey gtkspell gzip gzip-el h224 h281 h323 hal hash hdaps hddtemp hdf hdri hepmc hfs highlight highvolume history hotpixels hpn html http httpd httppower humanities hunspell hyphenation i18n ibmvio icc iconv icq icu id3 id3tag idb ieee1394 ifc ilbc image image-cache imagemagick imaging imap imlib indi infowidget inherit-graph inifile inkjar inotify int64 ioctl ipp iproute2 ipsec iptc iptv ipv6 irda iso14755 jabber jack jadetex java java5 java6 javacomm javamail javascript jbig jce jfs joystick jpeg jpeg2k json kate kdcraw kde kde-qt kdevplatform kerberos keyboard kino kipi kmail kolab konqueror kontact kpathsea krb4 l7filter ladspa lame lapack laptop largefile lastfm lastfmradio latex latex3 lcms ldb lensfun libass libcaca libgig libmms libnl libnotify libproxy libssh2 libsysfs libtiger libv4l libv4l2 libwww lightning live lm_sensors logitech-mouse logrotate logviewer lqr lyx lzma lzo m17n-lib mad mail mailbox maildir maildrop maps math mathml matplotlib matroska max-idx-128 mcve md5sum mdb meanwhile mfd-rewrites mjpeg mkl mmx mmxext mng modplug modules mono motif mp2 mp3 mp3tunes mp4 mpeg mpi mplayer mppe-mppc mpqc msn mssql mtp mudflap multilib multimedia musepack music mysql nas nautilus ncurses neXt network networkmanager nfs nfsv3 nfsv4 nis nls nova nptl nptlonly nsplugin ntfs ntp numeric numpy nut nuv nvidia nvram nvtv octave odbc ogg ogg123 ogm omega openal opencore-amr openct openexr opengl openmp openssl optimization optimized-qmake oscar otr pam parse-clocks pcmcia pcntl pcre pcsc-lite pdf pdo perl pg-intdatetime phonon php pkcs11 plasma player plotutils pm-utils png pnm policykit portaudio posix postgres postproc postscript ppds pppd preview-latex print ps pstoedit pstricks publishers pulseaudio pvr python qmake qt3support qt4 quicktime quota quotas radio ramfs rar raw rcs readline recording redeyes reflection reiserfs remote remoteosd replytolist resolvconf rle rpc rpm rss rtf rtsp ruby run-as-root samba sasl scanner schroedinger science sdl sdl-image secure-delete semantic-desktop sendmail sensord session sha1 shaders sharedext shine shout simplexml skey skins skype smartcard smbsharemodes smp sms smtp smux sndfile snmp sockets socks socks5 sound soundex sourceview spamassassin spamfilter speex spell spl sql sqlite sqlite3 sse sse2 sse3 sse4 sse4a sse5 ssh ssl ssse3 stream subversion suhosin suid svg swat sysfs syslog sysvipc szip t1lib taglib tcl tcpd tex tex4ht texmacs theora thinkpad threads thumbnail thumbnails thunderbird tidy tiff timezone tk tokenizer toolbar toolkit-scroll-bars totem transcode truetype tta tts tv tv_check tv_combiner tv_pick_cgi tvflash tvtime type3 udev udev-acl unicode unzip upnp usb utils v4l v4l2 vcd vcdinfo vcdx vdpau vga video vlm vorbis wav wavpack wcwidth wddx webcam webdav webdav-neon webdav-serf webinterface webkit webpresence websockets wicd wifi winbind winpopup wma wma-fixed wmf wordperfect wpd wpg wps wv2 wxwidgets x264 x264-static xanim xcomposite xemacs xetex xext xfs xft xhtml xim xine xinerama xinetd xml xmlpatterns xmlreader xmlrpc xmlwriter xmp xorg xpm xrender xsl xterm xterm-color xulrunner xv xvid xvmc yaz youtube yv12 zip zippy 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 authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache 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" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse joystick synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia svga vesa v4l fbdev vmware virtualbox" 
Comment 1 Sébastien Fabbro (RETIRED) gentoo-dev 2010-04-27 06:03:59 UTC
Hi Benjamin,

It looks like lapack-atlas related. Could you give the output of 
eselect list cblas, eselect list blas, and eselect list lapack?
Comment 2 Justin Lecher (RETIRED) gentoo-dev 2010-04-27 06:37:45 UTC
Probably related to 316863
Comment 3 Benjamin Schulz 2010-04-27 11:42:13 UTC

eselect cblas list
Installed CBLAS for library directory lib64
  [1]   atlas
  [2]   atlas-threads
  [3]   gsl *
Tux1 ~ # eselect blas list
Installed BLAS for library directory lib64
  [1]   atlas
  [2]   atlas-threads
  [3]   reference *
Tux1 ~ # eselect lapack list
Installed LAPACK for library directory lib64
  [1]   atlas *
  [2]   reference
Tux1 ~ # 
Comment 4 Sébastien Fabbro (RETIRED) gentoo-dev 2010-04-27 14:54:57 UTC
Could you try:

eselect blas atlas-threads
eselect cblas atlas-threads
and re-install both numpy and scipy.
Comment 5 Benjamin Schulz 2010-04-27 17:00:04 UTC
thanks. It works now.
Comment 6 Benjamin Schulz 2010-04-27 17:00:23 UTC
that is, I could emerge scipy
Comment 7 Sébastien Fabbro (RETIRED) gentoo-dev 2010-04-27 17:12:58 UTC
Ok, thanks for reporting.
In comment #4, I meant eselect {c,}blas set atlas-threads, but I guess you figured it out.