Bug 201192 – dev-python/numpy-1.0.4 fails to build with lapack useflag set

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Reinhard Kreim 2007-12-04 09:26:42 UTC]

If the "lapack" useflag is set, emerge of dev-python/numpy-1.0.4 fails.
Runs with no problem without the "lapack" useflag.

Reproducible: Always

Steps to Reproduce:
1.emerge -av numpy
2.
3.

Actual Results:  
creating build/temp.linux-i686-2.5/numpy/linalg
compile options: '-DNO_ATLAS_INFO=1 -Inumpy/core/include -Ibuild/src.linux-i686-2.5/numpy/core -Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
i686-pc-linux-gnu-gcc: numpy/linalg/lapack_litemodule.c
/usr/bin/gfortran -Wall -Wall -shared build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o -L/usr/lib -L/usr/lib -llapack -lblas -lpython2.5 -lgfortran -o build/lib.linux-i686-2.5/numpy/linalg/lapack_lite.so
/usr/lib/gcc/i686-pc-linux-gnu/4.2.2/../../../../i686-pc-linux-gnu/bin/ld: cannot find -llapack
collect2: ld gab 1 als Ende-Status zurück
/usr/lib/gcc/i686-pc-linux-gnu/4.2.2/../../../../i686-pc-linux-gnu/bin/ld: cannot find -llapack
collect2: ld gab 1 als Ende-Status zurück
error: Command "/usr/bin/gfortran -Wall -Wall -shared build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o -L/usr/lib -L/usr/lib -llapack -lblas -lpython2.5 -lgfortran -o build/lib.linux-i686-2.5/numpy/linalg/lapack_lite.so" failed with exit status 1





Portage 2.1.4_rc7 (default-linux/x86/2007.0/desktop, gcc-4.2.2, glibc-2.7-r0, 2.6.23-gentoo-r2 i686)
=================================================================
System uname: 2.6.23-gentoo-r2 i686 Intel(R) Core(TM)2 CPU T7600 @ 2.33GHz
Timestamp of tree: Tue, 04 Dec 2007 06:16:01 +0000
ccache version 2.4 [enabled]
app-shells/bash:     3.2_p17-r1
dev-java/java-config: 1.3.7, 2.1.3
dev-lang/python:     2.5.1-r4
dev-util/ccache:     2.4-r7
sys-apps/baselayout: 1.12.10-r5
sys-apps/sandbox:    1.2.18.1-r2
sys-devel/autoconf:  2.13, 2.61-r1
sys-devel/automake:  1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.18-r1
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   1.5.24
virtual/os-headers:  2.6.23-r2
ACCEPT_KEYWORDS="x86 ~x86"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=prescott -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /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/splash /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-O2 -march=prescott -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="ccache distlocks metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://gentoo.mirror.pw.edu.pl/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo"
LANG="de_DE.UTF8"
LC_ALL="de_DE.UTF-8"
LINGUAS="de"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="3dnow X X509 a52 aac aalib acl acpi akode alsa amr arts async audiofile automount avahi bash-completion berkdb bidi bitmap-fonts bl blas bonjour branding bzip2 cairo caps cblas cdda cddb cdio cdparanoia cdr chroot cli conntest cpudetection cracklib crypt cscope css cups curl custom-cflags daap dbus deprecated directfb divx dri dts dv dvd dvdr dvdread eds emboss enca encode esd evo extrafilters fam fame fbcon fbcondecor fbsplash ffmpeg fftw firefox flac fontconfig foomaticdb fortran fping ftp gadu gd gdbm ggi gif gimp glib glitz gmedia gnutls gpm groupwise gstreamer gtk gtkhtml hal hdaps hddtemp howl-compat hpn iconv icu idn imagemagick imap imlib immqt-bc inkjar ipv6 isdnlog jack java javascript jpeg jpeg2k kde kerberos krb4 lame lapack lcms ldap lesstif libcaca libnotify live logrotate lzo mad mailwrapper matroska mdnsresponder-compat meanwhile midi mikmod mjpeg mmx mmxext mng mod motif mp3 mpeg mpi mplayer msn mudflap musepack music musicbrainz mysql nas ncurses neXt network nls nntp nptl nptlonly nsplugin oav odbc ogg openal openexr opengl openmp oss pam pcre pdf perl php physfs plotutils png portaudio postgres povray ppds pppd prediction pyste python qq qt3 qt3support qt4 quicktime rar rdesktop readline real realmedia reflection regex remix rtc rtsp samba sametime sasl scanner scenarios sdl sdl-image sensord session shout silc skey skins slp sndfile songs speex spell spl sqlite sse sse2 ssl startup-notification stream subtitles svg svga swat syslog talkfilters tcl tcpd tetex tga themes theora threads tidy tiff timidity tk tools truetype truetype-fonts type1-fonts umfpack unicode usb utempter v4l v4l2 vcd vdr vidix vim-pager vim-syntax vim-with-x visualization voice vorbis wavpack wifi win32codecs winbind wmf wmp wxwindows x264 x86 xanim xcomposite xforms xine xinerama xml xorg xosd xpm xprint xv xvid xvmc yv12 zephyr zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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 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="keyboard mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de" USERLAND="GNU" VIDEO_CARDS="vesa fbdev"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Sébastien Fabbro (RETIRED) 2007-12-04 10:06:05 UTC]

Hi Reinhard,

Could you post the result of "eselect lapack list", "pkg-config --libs lapack", and "ls -l /usr/lib/liblapack*"?

Thanks

[Comment 2 Reinhard Kreim 2007-12-04 10:30:08 UTC]

I noticed that lapack-atlas was not installed. Though I have no idea why. 
I had to manually install lapack-atlas as it was not pulled in by dependency. 

Prior to that 

eselect lapack list listed only "reference" 

[Comment 3 Sébastien Fabbro (RETIRED) 2007-12-04 11:09:55 UTC]

> I noticed that lapack-atlas was not installed. Though I have no idea why. 
> I had to manually install lapack-atlas as it was not pulled in by dependency. 

You don't need lapack-atlas for a working numpy. lapack-reference is fine. If you really want to build with the *atlas, you will need the latest blas-atlas, lapack-atlas and make sure the eselect blas,cblas,atlas are set. 

What are the results of the other 2 commands I mentioned in comment #1?

[Comment 4 Reinhard Kreim 2007-12-04 14:27:06 UTC]

Ok found the bug, seems like lapack-atlas was installed earlier and then got removed by a system-update and a depclean. The links where not set correctly after it got removed.

A simply "eselect lapack set reference" did the job.

thx for the help

[Comment 5 Donnie Berkholz (RETIRED) 2007-12-04 20:30:56 UTC]

Looks like we might need something in the eselect module that we can run upon pkg_postrm() if it got uninstalled...