'emerge scilab' fails with: ... checking for sgemm_ in -lcomplib.sgimath... no checking for sgemm_ in -lblas... (cached) no checking for sgemm_ in -lblas... (cached) no configure: error: Impossible to find a BLAS compatible library (see BLAS or ATLAS).
Created attachment 278681 [details] /var/tmp/portage/sci-mathematics/scilab-5.3.2/work/scilab-5.3.2/config.log
root@orca:/usr/local/portage/sci-mathematics(262)# emerge --info =sci-mathematics/scilab-5.3.2 Portage 2.1.10.3 (default/linux/amd64/10.0/desktop, gcc-4.5.2, glibc-2.13-r2, 2.6.39-gentoo-r1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.39-gentoo-r1-x86_64-Intel-R-_Xeon-R-_CPU_W3520_@_2.67GHz-with-gentoo-2.0.3 Timestamp of tree: Thu, 30 Jun 2011 07:00:01 +0000 app-shells/bash: 4.2_p10 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2, 3.2 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: 1.9.6-r3, 1.10.3, 1.11.1-r1 sys-devel/binutils: 2.21.1 sys-devel/gcc: 4.4.5, 4.5.2 sys-devel/gcc-config: 1.4.1-r1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r1 sys-kernel/linux-headers: 2.6.38 (virtual/os-headers) sys-libs/glibc: 2.13-r2 Repositories: gentoo x11 java-overlay sunrise science bicatali x-portage 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="-march=native -O2 -pipe" 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="-march=native -O2 -pipe" 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="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr" MAKEOPTS="-j9" 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/x11 /var/lib/layman/java-overlay /var/lib/layman/sunrise /var/lib/layman/science /var/lib/layman/bicatali /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda 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 gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib 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 hvm hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy nvidia 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 samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4 ssl ssse3 startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thinkpad threads 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 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="braindump flow karbon kexi kpresenter krita tables words" CAMERAS="canon" 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="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" 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="nv nouveau 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 root@orca:/usr/local/portage/sci-mathematics(263)# emerge -pqv =sci-mathematics/scilab-5.3.2 [ebuild N ] sci-mathematics/scilab-5.3.2 USE="doc fftw gui matio nls tk umfpack xcos -hdf5"
I get this error on four of seven systems. On three systems configure comes successful to end. On one of this three systems even 'emerge scilab' comes to succesful to the end. On the three systems with succesful configure LAPACK is identified: checking for ATL_xerbla in -latlas... yes checking for sgemm_ in -lf77blas... yes checking for cblas_dgemm in -lcblas... yes Atlas found checking if LAPACK is available... checking for cheev_ in -latllapack -lf77blas -lm -latlas -lgslcblas ... yes LAPACK_LIBS env variable found ... BLAS/LAPACK/ATLAS Configuration: BLAS LIBS ............. = -lcblas -lf77blas -latlas BLAS TYPE ............. = Atlas LAPACK LIBS ........... = -latllapack -lf77blas -lm -latlas -lgslcblas LAPACK TYPE ........... = LAPACK_LIBS env variable At the four systems with the "Impossible to find a BLAS" error neither cblas nor blas is detected. Configure shows: ... checking for ATL_xerbla in -latlas... yes checking for sgemm_ in -lf77blas... yes checking for cblas_dgemm in -lcblas... no checking for sgemm_ in -lmkl... no checking for sgemm_ in -lblas... no checking for sgemm_ in -lcxml... no checking for sgemm_ in -ldxml... no checking for sgemm_ in -lscs... no checking for sgemm_ in -lcomplib.sgimath... no checking for sgemm_ in -lblas... (cached) no checking for sgemm_ in -lblas... (cached) no configure: error: Impossible to find a BLAS compatible library (see BLAS or ATLAS). At the three systems where LAPACK is identified via cblas I have the following links: root@moose:/root(9)# ll /usr/lib/libcblas.so* lrwxrwxrwx 1 root root 14 Jul 1 11:22 /usr/lib/libcblas.so -> libgslcblas.so* lrwxrwxrwx 1 root root 16 Jul 1 11:22 /usr/lib/libcblas.so.0 -> libgslcblas.so.0* On the other systems there are not such links. I suppose these links are remains of the old times of app-admin/eselect-1.2.15 and app-admin/eselect-cblas-0.1. Now, where eselect-cblas is blocked by sci-libs/atlas-3.9.41::bicatali, it seems me that there is not any tool (beside by creating this links manually) to set theese links: root@moose:/root(14)# eselect cblas list !!! Error: Can't load module cblas exiting root@moose:/root(15)# emerge -pvD eselect-cblas These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] app-admin/eselect-cblas-0.1 0 kB [0] [uninstall ] sci-libs/gsl-1.15-r1 USE="-static-libs" [1] [blocks B ] app-admin/eselect-cblas ("app-admin/eselect-cblas" is blocking sci-libs/atlas-3.9.41, sci-libs/gsl-1.15-r1) Total: 1 package (1 new, 1 uninstall), Size of downloads: 0 kB Conflict: 1 block (1 unsatisfied) Portage tree and overlays: [0] /usr/portage [1] /var/lib/layman/bicatali * Error: The above package list contains packages which cannot be * installed at the same time on the same system. (app-admin/eselect-cblas-0.1::gentoo, ebuild scheduled for merge) pulled in by eselect-cblas (sci-libs/atlas-3.9.41::bicatali, installed) pulled in by >=sci-libs/atlas-3.9.34 required by (virtual/cblas-2.0::bicatali, installed) >=sci-libs/atlas-3.8.4[lapack] required by (virtual/lapack-3.3::bicatali, installed) ... Any suggestions?
there was a recent change in the cmake-utils.eclass. This most probably fixed the issue. Try updating cmake to latest version and check again.
I have cmake-2.8.5-r2 it fixed opencv and gromacs. I suppose it is the newest version or am I mistaken?
The eselect-{cblas,blas,lapack} are not needed since the new bicatali overlay ebuild for atlas use the aternative eclass which generates the eselect modules on the fly. Make sure you don't have any stray links left over when you remove the eselect-{cblas,blas,lapack} packages, and everything should be set up fine. There is a bug in the scilab configure script right now, I've submitted this bug upstream: http://bugzilla.scilab.org/show_bug.cgi?id=9824 We actually have export BLAS_LIBS=$(pkg-config --libs blas) in the scilab ebuild, so it should work fine when upstream fixes it. That being said, the atlas version in the bicatali overlay is completely unsupported, and produces non-working builds in many cases (missing symbols).
Please check with the new ebuild that I pushed to the science overlay, it should work now.
fixed a while ago. thanks Guillaume.
