| Summary: | dev-python/numpy-1.6.1 because of atlas problems | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
| Component: | [OLD] Library | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | RESOLVED INVALID | ||
| Severity: | normal | CC: | jlec, python |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
Please attach full Bild.log. which blas/lapack are you using? I assume this is the same problem as bug 380723 . please reopen if not |
revdep-rebuild fails, because numpy is not emerged. 'emerge numpy' fails with: ... Running from numpy source directory.F2PY Version 2 blas_opt_info: blas_mkl_info: 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 NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS /var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/system_info.py:528: UserWarning: Specified path is invalid. warnings.warn('Specified path %s is invalid.' % d) Setting PTATLAS=ATLAS customize GnuFCompiler Could not locate executable g77 Could not locate executable f77 customize IntelFCompiler Could not locate executable ifort Could not locate executable ifc customize LaheyFCompiler Could not locate executable lf95 customize PGroupFCompiler Could not locate executable pgf90 Could not locate executable pgf77 customize AbsoftFCompiler Could not locate executable f90 customize NAGFCompiler Could not locate executable f95 customize VastFCompiler customize CompaqFCompiler Could not locate executable fort customize IntelItaniumFCompiler Could not locate executable efort Could not locate executable efc customize IntelEM64TFCompiler customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using config compiling '_configtest.c': /* This file is generated from numpy/distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: x86_64-pc-linux-gnu-gcc -O2 -march=k8 -O2 -march=k8 -fno-strict-aliasing -fPIC compile options: '-c' x86_64-pc-linux-gnu-gcc: _configtest.c x86_64-pc-linux-gnu-gcc -O2 -march=k8 _configtest.o -L/usr/lib64 -o _configtest _configtest.o: In function `main': _configtest.c:(.text+0x5): undefined reference to `ATL_buildinfo' collect2: ld returned 1 exit status _configtest.o: In function `main': _configtest.c:(.text+0x5): undefined reference to `ATL_buildinfo' collect2: ld returned 1 exit status failure. removing: _configtest.c _configtest.o Status: 255 Output: compiling '_configtest.c': /* This file is generated from numpy/distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: x86_64-pc-linux-gnu-gcc -O2 -march=k8 -O2 -march=k8 -fno-strict-aliasing -fPIC compile options: '-c' x86_64-pc-linux-gnu-gcc: _configtest.c x86_64-pc-linux-gnu-gcc -O2 -march=k8 _configtest.o -L/usr/lib64 -o _configtest _configtest.o: In function `main': _configtest.c:(.text+0x5): undefined reference to `ATL_buildinfo' collect2: ld returned 1 exit status Setting PTATLAS=ATLAS FOUND: libraries = [] library_dirs = ['/usr/lib64'] language = c define_macros = [('ATLAS_INFO', '"\\"None\\""')] FOUND: libraries = [] library_dirs = ['/usr/lib64'] language = c define_macros = [('ATLAS_INFO', '"\\"None\\""')] lapack_opt_info: lapack_mkl_info: mkl_info: 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 NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries lapack not found in /usr/lib64 numpy.distutils.system_info.atlas_threads_info Setting PTATLAS=ATLAS Traceback (most recent call last): File "setup.py", line 196, in <module> setup_package() File "setup.py", line 189, in setup_package configuration=configuration ) File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 142, in configuration config.add_subpackage('numpy') File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "numpy/setup.py", line 14, in configuration config.add_subpackage('linalg') File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "numpy/linalg/setup.py", line 12, in configuration lapack_info = get_info('lapack_opt',0) # and {} File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/system_info.py", line 311, in get_info return cl().get_info(notfound_action) File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/system_info.py", line 456, in get_info self.calc_info() File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/system_info.py", line 1314, in calc_info atlas_info = get_info('atlas_threads') File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/system_info.py", line 311, in get_info return cl().get_info(notfound_action) File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/system_info.py", line 456, in get_info self.calc_info() File "/var/tmp/portage/dev-python/numpy-1.6.1/work/numpy-1.6.1/numpy/distutils/system_info.py", line 986, in calc_info lapack_name = lapack['libraries'][0] IndexError: list index out of range * ERROR: dev-python/numpy-1.6.1 failed (compile phase): Reproducible: Always root@grizzly:/usr/src(30)# emerge --info =dev-python/numpy-1.6.1 Portage 2.1.10.11 (default/linux/amd64/10.0/desktop, gcc-4.5.3, glibc-2.13-r4, 3.0.3 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.0.3-x86_64-AMD_Athlon-tm-_64_Processor_3200+-with-gentoo-2.0.3 Timestamp of tree: Thu, 25 Aug 2011 10:30:01 +0000 app-shells/bash: 4.2_p10 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2-r2, 3.2-r2 dev-util/cmake: 2.8.5-r2::science 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 java-overlay lordvan science x11 sunrise arcon local x-cpan g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=k8" CHOST="x86_64-pc-linux-gnu" 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="-O2 -march=k8" DISTDIR="/usr/portage/distfiles" 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" FFLAGS="-O2 -march=k8" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ " LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" 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/java-overlay /var/lib/layman/lordvan /var/lib/layman/science /var/lib/layman/x11 /var/lib/layman/sunrise /var/lib/layman/arcon /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding 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 dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago garmin 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 hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kde kdrive kerberos kpathsea ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc 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 neXt 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 pae pam pango 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 sms sndfile snmp soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 video virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets x264 xattr xcb xemacs xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml 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 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="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" DVB_CARDS="tda10046 saa7134" 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" LIRC_DEVICES="hauppauge_dvb" 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" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= dev-python/numpy-1.6.1 was built with the following: USE="doc lapack (multilib) -test" LDFLAGS="-Wl,-O1 -Wl,--as-needed -shared" root@grizzly:/usr/src(31)# emerge -pqv =dev-python/numpy-1.6.1 [ebuild R ] dev-python/numpy-1.6.1 USE="doc lapack -test"