Bug 391337 – sci-libs/scipy-0.9.0-r1 fails tests

• Product: Gentoo Linux
• Status: RESOLVED DUPLICATE

[Description Paweł Hajdan, Jr. (RETIRED) 2011-11-22 07:47:12 UTC]

Created attachment 293381 [details]
build.log.gz

======================================================================
ERROR: Failure: ImportError (scipy/linalg/clapack.so: undefined symbol: clapack_sgesv)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "scipy/interpolate/__init__.py", line 13, in <module>
    from rbf import Rbf
  File "scipy/interpolate/rbf.py", line 48, in <module>
    from scipy import linalg
  File "scipy/linalg/__init__.py", line 9, in <module>
    from basic import *
  File "scipy/linalg/basic.py", line 14, in <module>
    from lapack import get_lapack_funcs
  File "scipy/linalg/lapack.py", line 15, in <module>
    from scipy.linalg import clapack
ImportError: scipy/linalg/clapack.so: undefined symbol: clapack_sgesv

======================================================================
ERROR: Failure: AttributeError ('module' object has no attribute 'byteordercodes')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/test-2.7/lib/python/scipy/io/matlab/tests/test_byteordercodes.py", line 7, in <module>
    import scipy.io.matlab.byteordercodes as sibc
AttributeError: 'module' object has no attribute 'byteordercodes'

======================================================================
ERROR: Failure: AttributeError ('module' object has no attribute 'byteordercodes')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/test-2.7/lib/python/scipy/io/matlab/tests/test_mio.py", line 38, in <module>
    import scipy.io.matlab.byteordercodes as boc
AttributeError: 'module' object has no attribute 'byteordercodes'

======================================================================
ERROR: Failure: AttributeError ('module' object has no attribute 'byteordercodes')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/test-2.7/lib/python/scipy/io/matlab/tests/test_mio5_utils.py", line 23, in <module>
    import scipy.io.matlab.byteordercodes as boc
AttributeError: 'module' object has no attribute 'byteordercodes'

======================================================================
ERROR: Failure: ImportError (scipy/lib/lapack/clapack.so: undefined symbol: clapack_sgesv)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "scipy/lib/lapack/__init__.py", line 16, in <module>
    import clapack
ImportError: scipy/lib/lapack/clapack.so: undefined symbol: clapack_sgesv

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "scipy/linalg/__init__.py", line 9, in <module>
    from basic import *
  File "scipy/linalg/basic.py", line 14, in <module>
    from lapack import get_lapack_funcs
  File "scipy/linalg/lapack.py", line 14, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: NameError (name 'pilutil' is not defined)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "scipy/misc/__init__.py", line 16, in <module>
    __all__ += pilutil.__all__
NameError: name 'pilutil' is not defined

======================================================================
ERROR: Failure: AttributeError ('module' object has no attribute 'blas')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "scipy/sparse/linalg/__init__.py", line 5, in <module>
    from isolve import *
  File "scipy/sparse/linalg/isolve/__init__.py", line 6, in <module>
    from lgmres import lgmres
  File "scipy/sparse/linalg/isolve/lgmres.py", line 5, in <module>
    import scipy.lib.blas as blas
AttributeError: 'module' object has no attribute 'blas'

FAILED (KNOWNFAIL=3, SKIP=8, errors=20)
Running unit tests for scipy
NumPy version 1.6.0
NumPy is installed in /usr/lib/python2.7/site-packages/numpy
SciPy version 0.9.0
SciPy is installed in scipy
Python version 2.7.2 (default, Nov  6 2011, 18:24:55) [GCC 4.5.3]
nose version 1.1.2
 * ERROR: sci-libs/scipy-0.9.0-r1 failed (test phase):
 *   test failed

(there are more failures)


Portage 2.1.10.11 (default/linux/x86/10.0/developer, gcc-4.5.3, glibc-2.12.2-r0, 3.0.6-gentoo i686)
=================================================================
System uname: Linux-3.0.6-gentoo-i686-Intel-R-_Core-TM-2_Duo_CPU_P8700_@_2.53GHz-with-gentoo-2.0.3
Timestamp of tree: Mon, 21 Nov 2011 12:00:01 +0000
app-shells/bash:          4.1_p9
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r3, 3.1.4-r3
dev-util/cmake:           2.8.4-r1
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:       1.10.3, 1.11.1
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:           2.12.2
Repositories: gentoo x-portage
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="*"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=i686 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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 -march=i686 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs collision-protect compress-build-logs distlocks ebuild-locks fixlafiles fixpackages multilib-strict news parallel-fetch protect-owned sandbox sfperms sign splitdebug strict test test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LDFLAGS="-Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa berkdb bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus device-mapper dri dts dvd dvdr emacs emboss encode exif fam firefox flac fortran gdbm gdu gif git gnome-keyring gnutls gtk iconv icu jpeg lcms libnotify mad mbox mercurial mng modules mp3 mp4 mpeg mudflap ncurses nls nptl nptlonly nss ogg opengl openmp pam pango pcre pdf perl png policykit ppds pppd python qt3support readline sdl secure-delete session snmp spell sqlite ssl startup-notification subversion svg sysfs tcb tcpd threads tiff toolkit-scroll-bars truetype udev unicode usb vorbis x264 x86 xcb xft xinerama xml xorg xulrunner xv xvfb xvid zlib" ALSA_CARDS="ens1371" 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 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="evdev keyboard vmmouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vmware vesa vga" 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, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 François Bissey 2011-11-22 11:10:57 UTC]

Smells like a remnant of #371099

[Comment 2 Justin Lecher (RETIRED) 2013-02-07 13:44:35 UTC]

*** This bug has been marked as a duplicate of bug 413515 ***