'emerge mayavi' fails with: ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-visualization/mayavi-3.3.0/work/Mayavi-3.3.0 ... python2.6 setup.py build Traceback (most recent call last): File "setup.py", line 70, in <module> import numpy File "/usr/lib64/python2.6/site-packages/numpy/__init__.py", line 132, in <module> import add_newdocs File "/usr/lib64/python2.6/site-packages/numpy/add_newdocs.py", line 9, in <module> from lib import add_newdoc File "/usr/lib64/python2.6/site-packages/numpy/lib/__init__.py", line 13, in <module> from polynomial import * File "/usr/lib64/python2.6/site-packages/numpy/lib/polynomial.py", line 17, in <module> from numpy.linalg import eigvals, lstsq File "/usr/lib64/python2.6/site-packages/numpy/linalg/__init__.py", line 47, in <module> from linalg import * File "/usr/lib64/python2.6/site-packages/numpy/linalg/linalg.py", line 22, in <module> from numpy.linalg import lapack_lite ImportError: /usr/lib/liblapack.so.0: undefined symbol: clapack_ilaenv /usr/lib/liblapack.so.0 is a link to /usr/lib/lapack/atlas/liblapack.so. LAPACK atlas is the eselected lapack package: root@moose:/root(49)# eselect lapack list Installed LAPACK for library directory lib64 [1] atlas * [2] reference Also reemerging of lapack-atlas does not solve the problem. Reproducible: Always root@moose:/root(50)# emerge --info =sci-visualization/mayavi-3.3.0 Portage 2.1.7.16 (default/linux/amd64/10.0/desktop, gcc-4.4.2, glibc-2.11-r1, 2.6.32-gentoo-r1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.32-gentoo-r1-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.0.1 Timestamp of tree: Tue, 26 Jan 2010 10:00:01 +0000 app-shells/bash: 4.0_p37 dev-java/java-config: 2.1.10 dev-lang/python: 2.6.4, 3.1.1-r1 dev-python/pycrypto: 2.1.0 dev-util/cmake: 2.8.0-r1 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.6.0-r1 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe" CHOST="x86_64-pc-linux-gnu" 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="-O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" FFLAGS="-march=nocona -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LDFLAGS="-Wl,-O1" LINGUAS="de fr" MAKEOPTS="-j1" 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="/var/lib/layman/science /var/lib/layman/x11 /var/lib/layman/n4g /var/lib/layman/java-overlay /var/lib/layman/zugaina /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit X Xaw3d a52 aac acl acpi administrator afs alsa amd64 ao aotuv apache2 asf aspell atlas audacious audiofile automount bash-completion beagle berkdb blas bluetooth boo boost branding bzip2 c++ cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib crypt cups curl cxx daap dbus device-mapper dga dia djvu doc dri ds2490 dts dv dvb dvd dvdr dvi dxr3 eds elf emacs emboss encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk foomaticdb fortran fpx fts3 fuse galago garmin gd gdal gdbm geolocation geos gif gimp ginac git glade glib glitz gml gmp gnokii gnome gnome-keyring gnuplot gnutls gphoto2 gpm graphics graphtft graphviz gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb ipod ipv6 irda ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kde kerberos kexi kpathsea kvm ladspa lame lapack latex lcms ldap libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mailwrapper math matroska mikmod mmx mmxext mng modules mono motif mozdevelop mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python qhull qt3support qt4 quicktime readline reflection reiserfs rle romio rpc rrdcgi rrdtool samba sasl science sdl server session slang slp smbclient smp sndfile snmp soup sox speex spell spl sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora threads thunar thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" 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 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" ELIBC="glibc" 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" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS root@moose:/root(51)# emerge -pqv =sci-visualization/mayavi-3.3.0 [ebuild N ] sci-visualization/mayavi-3.3.0 USE="doc qt4"
Did you run revdep-rebuild?
Yes I did.
Thanks, reassigning on maintainers.
Hi, What is the ouput of your numpy installation testing? You can run it with: python -c "import numpy; numpy.test()"
Juergen, since you're using lapack-atlas please make sure that you've selected atlas' cblas also # eselect cblas set atlas The problem is that clapack_ilaenv is part of atlas' cblas, so lapack-atlas presently will only link again this cblas implementation. I wonder if we can move it into the lapack *.so somehow. Markus
Thanks Markus, that was the reason: blas atlas-threads, lapack was set to atlas but cblas was set to reference. After setting cblas to atlas-threads. I could emerge mayavi and the first start was also succesful. Regards
After setting cblas to atlas-threads I still tried: root@moose:/root(206)# python -c "import numpy; numpy.test()" Running unit tests for numpy Traceback (most recent call last): File "<string>", line 1, in <module> File "/usr/lib64/python2.6/site-packages/numpy/testing/nosetester.py", line 326, in test self._show_system_info() File "/usr/lib64/python2.6/site-packages/numpy/testing/nosetester.py", line 187, in _show_system_info nose = import_nose() File "/usr/lib64/python2.6/site-packages/numpy/testing/nosetester.py", line 69, in import_nose raise ImportError(msg) ImportError: Need nose >= 0.10.0 for tests - see http://somethingaboutorange.com/mrl/projects/nose I installed dev-python/nose. And tried once more: root@moose:/root(210)# python -c "import numpy; numpy.test()" Running unit tests for numpy NumPy version 1.4.0 NumPy is installed in /usr/lib64/python2.6/site-packages/numpy Python version 2.6.4 (r264:75706, Jan 27 2010, 14:47:16) [GCC 4.4.2] nose version 0.11.1 ...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K........................................................................................K......................K.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. ---------------------------------------------------------------------- Ran 2490 tests in 7.735s OK (KNOWNFAIL=3)
So this is fixed. However, let's not forget: > The problem is that clapack_ilaenv is part of atlas' cblas, > so lapack-atlas presently will only link again this cblas > implementation. I wonder if we can move it into the > lapack *.so somehow. > > Markus >
