| Summary: | liblapack.so: undefined reference to ATL_sgelq2 and atl_f77wrap_zgelqf_ | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
| Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | RESOLVED OBSOLETE | ||
| Severity: | normal | CC: | graphics+disabled, nadavh, nowa, vejmema1 |
| Priority: | High | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: | /var/tmp/portage/media-gfx/hugin-2010.0.0_rc1/temp/build.log | ||
Created attachment 222681 [details]
/var/tmp/portage/media-gfx/hugin-2010.0.0_rc1/temp/build.log
root@orca:/root(22)# eselect lapack list Installed LAPACK for library directory lib64 [1] atlas * [2] reference root@orca:/root(23)# eselect blas list Installed BLAS for library directory lib64 [1] atlas [2] atlas-threads * [3] reference Getting the error:
$ ImportError: /usr/lib/liblapack.so.0: undefined symbol: ATL_dgelq2
at the python prompt after:
>> import numpy
after the upgrade to sci-libs/lapack-atlas-3.9.23-r1
For me it compiled well. So you can compare the differences:
17:13:53 martin@myhost ~ $ emerge --info =media-gfx/hugin-2010.0.0_rc1
Portage 2.1.7.17 (default/linux/amd64/10.0, gcc-4.3.4, glibc-2.10.1-r1, 2.6.31-gentoo-r6-CUSTOM x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-2.6.31-gentoo-r6-CUSTOM-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T6400_@_2.00GHz-with-gentoo-1.12.13
Timestamp of tree: Tue, 09 Mar 2010 14:00:01 +0000
distcc 3.1 x86_64-pc-linux-gnu [disabled]
ccache version 2.4 [enabled]
app-shells/bash: 4.0_p35
dev-java/java-config: 2.1.10
dev-lang/python: 2.4.6, 2.5.4-r4, 2.6.4-r1
dev-python/pycrypto: 2.1.0_beta1
dev-util/ccache: 2.4-r7
dev-util/cmake: 2.6.4-r3
sys-apps/baselayout: 1.12.13
sys-apps/sandbox: 1.6-r2
sys-devel/autoconf: 2.13, 2.63-r1
sys-devel/automake: 1.9.6-r2, 1.10.3
sys-devel/binutils: 2.18-r3
sys-devel/gcc: 3.4.6-r2, 4.3.4
sys-devel/gcc-config: 1.4.1
sys-devel/libtool: 2.2.6b
virtual/os-headers: 2.6.30-r1
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA dlj-1.1 skype-eula"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -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/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=core2 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests ccache distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch"
GENTOO_MIRRORS="http://gentoo.mirror.web4u.cz/ ftp://gentoo.mirror.web4u.cz/"
LANG="cs_CZ.UTF-8"
LDFLAGS="-Wl,-O1"
LINGUAS="cs en"
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/layman/sunrise /usr/local/portage/layman/emacs /usr/local/portage/layman/turbogears2 /usr/local/portage/layman/zugaina /usr/local/portage/layman/gnome /usr/local/portage/layman/lila-theme /usr/local/overlay"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 acl acpi alsa amd64 apache2 avahi bbdb berkdb branding bzip2 cairo cli cracklib crypt ctype cups cupsddk curl cxx dbus dia directfb dri dvb dvd emacs encode enscript exif ffmpeg firefox flac fortran gd gdbm gif gimp gmplayer gnome gpm gstreamer gtk hal iconv id3 id3tag imagemagick imap inifile ipv6 jadetex java jpeg json kpathsea lame ldap mdnsresponder-compat mmx modules mozilla mp3 mpeg mudflap multilib mysql mysqli ncurses networkmanager nls nptl nptlonly nsplugin objc ogg opengl openmp pam pcre pdo perl planner plotutils png posix postscript pppd pulseaudio python qt3support raw readline reflection samba session simplexml skins spl sqlite sse sse2 ssl subversion suexec svg sysfs tcpd tex theora threads tidy tiff tokenizer truetype unicode usb vcdx vorbis xml xmlreader xmlrpc xmlwriter xorg xsl xulrunner zip zlib" 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 unicode" APACHE2_MPMS="prefork" CAMERAS="canon" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="cs en" NETBEANS_MODULES="apisupport harness ide java nb websvccommon enterprise groovy php ruby webcommon cnd dlight ergonomics identity mobility profiler" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vga vesa intel"
Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
=================================================================
Package Settings
=================================================================
media-gfx/hugin-2010.0.0_rc1 was built with the following:
USE="(multilib) sift -lapack" LINGUAS="cs -bg -ca -de -en_GB -es -fr -hu -it -ja -ko -nl -pl -pt_BR -ru -sk -sl -sv -uk -zh_CN -zh_TW"
Now it compiles for me too. I suppose its due to the downgrade of lapack-atlas:
root@orca:/root(14)# genlop -t lapack-atlas | tail
Fri Feb 19 13:31:56 2010 >>> sci-libs/lapack-atlas-3.9.23
merge time: 5 minutes and 59 seconds.
Mon Mar 8 13:02:14 2010 >>> sci-libs/lapack-atlas-3.9.23-r1
merge time: 6 minutes and 1 second.
Tue Mar 9 19:51:06 2010 >>> sci-libs/lapack-atlas-3.9.23
merge time: 6 minutes.
root@orca:/root(12)# genlop -t hugin
* media-gfx/hugin
Tue Jan 26 11:36:00 2010 >>> media-gfx/hugin-2009.4.0
merge time: 9 minutes and 27 seconds.
Thu Mar 4 15:34:13 2010 >>> media-gfx/hugin-2009.4.0
merge time: 9 minutes and 3 seconds.
Tue Mar 9 20:09:05 2010 >>> media-gfx/hugin-2010.0.0_rc1
merge time: 9 minutes and 13 seconds.
As it is seen from genlop -t, I did my last attempt to emerge hugin-2010.0.0_rc1, which fails, with lapack-atlas-3.9.23-r1.
Per Comment #3 this is happening also with dev-python/numpy and the undefined references are from liblapack.so, so doesn't seem like a bug in hugin to me... (In reply to comment #5) > Now it compiles for me too. I suppose its due to the downgrade of lapack-atlas: > root@orca:/root(14)# genlop -t lapack-atlas | tail > > Fri Feb 19 13:31:56 2010 >>> sci-libs/lapack-atlas-3.9.23 > merge time: 5 minutes and 59 seconds. > > Mon Mar 8 13:02:14 2010 >>> sci-libs/lapack-atlas-3.9.23-r1 > merge time: 6 minutes and 1 second. > > Tue Mar 9 19:51:06 2010 >>> sci-libs/lapack-atlas-3.9.23 > merge time: 6 minutes. 6minutes for atlas is to short. This looks like http://sourceforge.net/tracker/index.php?func=detail&aid=3301697&group_id=23725&atid=379483 ATLAS bug. I don't know why Python is cc'ed in on this bug. @sci: I'd close this report and mark it as OBSOLETE. |
'emerge hugin' fails with: ... cd /var/tmp/portage/media-gfx/hugin-2010.0.0_rc1/work/hugin-2010.0.0_build/src/celeste && /usr/bin/cmake -E cmake_link_script CMakeFiles/celeste_standalone.dir/link.txt --verbose=TRUE /usr/bin/x86_64-pc-linux-gnu-g++ -march=core2 -msse4 -mcx16 -msahf -O2 -pipe -O3 -Wl,-O1 CMakeFiles/celeste_standalone.dir/Main.cpp.o -o celeste_standalone -rdynamic libceleste.so.0.0 ../foreign/vigra/vigra_impex/libhuginvigraimpex.so.0.0 -lImath -lIlmImf -lIex -lHalf -lIlmThread -ljpeg -ltiff -lpng -lz -lz -lexiv2 -lboost_thread-mt-1_42 -L/usr/lib64 -pthread -Wl,-O1 -L/usr/lib64 -lwx_baseu-2.8 -lwx_gtk2u_core-2.8 -lwx_gtk2u_xrc-2.8 -lwx_gtk2u_html-2.8 -lwx_baseu_xml-2.8 -lwx_gtk2u_adv-2.8 -lwx_gtk2u_gl-2.8 -lwx_baseu_net-2.8 ../hugin1/base_wx/libhuginbasewx.a ../hugin_base/libhuginbase.so.0.0 ../foreign/vigra/vigra_impex/libhuginvigraimpex.so.0.0 -lImath -lIlmImf -lIex -lHalf -lIlmThread -ljpeg -lpng -lz -ltiff -lexiv2 -lboost_thread-mt-1_42 -lGLU -lGL -lSM -lICE -lX11 -lXext -lpano13 -llapack -lblas -lGLEW ../foreign/levmar/libhuginlevmar.a -Wl,-rpath,/var/tmp/portage/media-gfx/hugin-2010.0.0_rc1/work/hugin-2010.0.0_build/src/celeste:/var/tmp/portage/media-gfx/hugin-2010.0.0_rc1/work/hugin-2010.0.0_build/src/foreign/vigra/vigra_impex:/var/tmp/portage/media-gfx/hugin-2010.0.0_rc1/work/hugin-2010.0.0_build/src/hugin_base: /usr/lib64/liblapack.so: undefined reference to `ATL_sgelq2' /usr/lib64/liblapack.so: undefined reference to `ATL_dgelq2' /usr/lib64/liblapack.so: undefined reference to `ATL_zgelq2' /usr/lib64/liblapack.so: undefined reference to `ATL_cgelq2' /usr/lib64/liblapack.so: undefined reference to `atl_f77wrap_zgelqf_' /usr/lib64/liblapack.so: undefined reference to `atl_f77wrap_cgelqf_' /usr/lib64/liblapack.so: undefined reference to `atl_f77wrap_sgelqf_' /usr/lib64/liblapack.so: undefined reference to `atl_f77wrap_dgelqf_' collect2: ld returned 1 exit status Reproducible: Always root@orca:/root(18)# emerge --info =media-gfx/hugin-2010.0.0_rc1 Portage 2.1.8.1 (default/linux/amd64/10.0/desktop, gcc-4.4.3, glibc-2.11-r1, 2.6.32-gentoo-r7 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.32-gentoo-r7-x86_64-Intel-R-_Xeon-R-_CPU_W3520_@_2.67GHz-with-gentoo-2.0.1 Timestamp of tree: Mon, 08 Mar 2010 10:30:01 +0000 app-shells/bash: 4.1_p2 dev-java/java-config: 2.1.10 dev-lang/python: 2.6.4-r1, 3.1.1-r1 dev-python/pycrypto: 2.1.0 dev-util/cmake: 2.8.0-r2 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: 2.20.1 sys-devel/gcc: 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 PUEL dlj-1.1 skype-eula" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=core2 -msse4 -mcx16 -msahf -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="-march=core2 -msse4 -mcx16 -msahf -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org" 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/zugaina /var/lib/layman/java-overlay /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit X Xaw3d a52 aac abiword acl acpi administrator afs alsa amd64 ao aotuv apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost branding bzip2 c++ cairo cdda cddb cdf cdio cdparanoia cdr cdrkit cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus designer devhelp device-mapper dga dia djvu doc dri ds2490 dts dv dvb dvd dvdr dvi eds elf emacs emboss empathy encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk foomaticdb fortran fpx fts3 fuse galago gcj gd gdal gdbm geolocation geos gif gimp ginac git glade glib glitz gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hdri hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kde kdrive kerberos kexi kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mailwrapper mapnik math matroska mikmod mkl mmx mmxext mng modules mono moonlight 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 secure-delete semantic-desktop server session sip 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 thinkpad threads thunar thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit 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 nouveau vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS root@orca:/root(19)# emerge -pqv =media-gfx/hugin-2010.0.0_rc1 [ebuild U ] media-gfx/hugin-2010.0.0_rc1 [2009.4.0] USE="lapack sift" LINGUAS="de fr -bg -ca -cs -en_GB -es -hu -it -ja -ko -nl -pl -pt_BR -ru -sk -sl -sv -uk -zh_CN -zh_TW"