Bug 404237 – [science overlay]sci-libs/lapack-reference-3.4.0_p20120215 failed to link: -lblas not found.

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Mathieu Z 2012-02-17 11:05:42 UTC]

sci-lib/blas-reference installs /usr/lib64/librefblas.so, while sci-libs/lapack-reference looks for libblas.so to link. So linking fails. It's either missing symlink for blas-reference or some issue with the configuration script of lapack-reference.

Reproducible: Always

Steps to Reproduce:
1. emerge lapack-reference
2.
3.
Actual Results:  
Building Fortran object SRC/CMakeFiles/reflapack.dir/zlarscl2.f.o
[ 99%] Building Fortran object SRC/CMakeFiles/reflapack.dir/zlascl2.f.o
[100%] Building Fortran object SRC/CMakeFiles/reflapack.dir/zla_wwaddw.f.o
Linking Fortran shared library ../lib/libreflapack.so
/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lblas
collect2: ld returned 1 exit status
make[2]: *** [lib/libreflapack.so] Error 1
make[1]: *** [SRC/CMakeFiles/reflapack.dir/all] Error 2
make: *** [all] Error 2
 * ERROR: sci-libs/lapack-reference-3.4.0_p20120215 failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of 'emerge --info =sci-libs/lapack-reference-3.4.0_p20120215',
 * the complete build log and the output of 'emerge -pqv =sci-libs/lapack-reference-3.4.0_p20120215'.
 * This ebuild is from an overlay named 'science': '/var/lib/layman/science/'
 * The complete build log is located at '/var/log/portage/build/sci-libs/lapack-reference-3.4.0_p20120215:20120217-001041.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/lapack-reference-3.4.0_p20120215/temp/environment'.
 * S: '/var/tmp/portage/sci-libs/lapack-reference-3.4.0_p20120215/work/lapack-3.4.0_p20120215'


$ emerge --info
Portage 2.2.0_alpha86 (default/linux/amd64/10.0, gcc-4.5.3, glibc-2.14.1-r2, 3.2.1-ck x86_64)
=================================================================
System uname: Linux-3.2.1-ck-x86_64-Intel-R-_Core-TM-_i7_CPU_L_620_@_2.00GHz-with-gentoo-2.1
Timestamp of tree: Thu, 16 Feb 2012 21:30:01 +0000
ccache version 3.1.7 [enabled]
app-shells/bash:          4.2_p20
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r3, 3.2.2
dev-util/ccache:          3.1.7
dev-util/cmake:           2.8.7-r3
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1
sys-apps/openrc:          0.9.8.4
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.3
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.5.3-r2
sys-devel/gcc-config:     1.5-r2
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r3
sys-kernel/linux-headers: 3.2 (virtual/os-headers)
sys-libs/glibc:           2.14.1-r2
Repositories: x11 lisp science desktop-effects gentoo-zh gentoo-haskell sunrise java-overlay cj-overlay mz-overlay gentoo
Installed sets: 
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -fomit-frame-pointer -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -fomit-frame-pointer -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--keep-going --quiet-build n"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fail-clean fixlafiles metadata-transfer news parallel-fetch preserve-libs protect-owned sandbox sfperms sign split-elog split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr"
FFLAGS=""
GENTOO_MIRRORS="http://distro.ibiblio.org/pub/linux/distributions/gentoo/ http://gentoo.osuosl.org/ http://ftp.ucsb.edu/pub/mirrors/linux/gentoo/"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-O2 -Wl,--hash-style=both"
LINGUAS="en ja zh zh_CN zh_TW en_US en_GB"
MAKEOPTS="-j4 --load-average"
PKGDIR="/usr/portage//packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/lisp /var/lib/layman/science /var/lib/layman/desktop-effects /var/lib/layman/gentoo-zh /var/lib/layman/haskell /var/lib/layman/sunrise /var/lib/layman/java-overlay /var/lib/layman/cj-overlay /usr/local/portage /usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext X a52 aac aalib acl acpi aim alsa amd64 apache2 audiofile avahi bash-completion bcmath berkdb bidi bittorrent blas bluetooth branding bzip2 cairo calendar caps ccache cdaudio cdda chm cjk cleartype cli clisp consolekit cracklib crypt cscope css ctype cups curl curlwrappers cxx dbus dbx dga dhcpcd directfb djvu dri dts dv dvd dvdread dvi ebook eds emacs emacs-w3 encode enscript evo exif expat faac fam fastcgi fbcon ffmpeg fftw flac flash fontconfig foomaticdb fortran freetds ftp fuse gallium gcl gconf gd gdbm ginac git glib glitz glut gmp gnome gnome-keyring gnuplot gnutls gpg gphoto2 gpm gps gs gsl gstreamer gtk gtk3 gtkhtml gzip hdaps highlight httpd iconv icq icu idn ieee1394 imagemagick imap imlib innodb inotify introspection ipod ipv6 jabber java javascript joystick jpeg jpeg2k kpathsea lame lapack laptop latex latex3 lcms libcaca libnotify llvm lm_sensors lua luatex lzma m17n-lib mad matroska mercurial mime mmx mmxext mng modplug modules mp3 mp4 mpeg mpi mplayer msn mtp mudflap multilib musepack musicbrainz mysql mysqli nautilus ncurses netboot networkmanager nis nls nntp nptl nptlonly nsplugin nss ntp odbc ogg openal openexr opengl openmp openntpd openssl osc oscar pae pam pch pcre pda pdf plotutils png policykit posix postgres ppds pppd pulseaudio qq qt3support qt4 quicktime rar rcs readline recode resolvconf rss rtmp samba sasl scanner sdl session simplexml slang sndfile snmp sockets socks5 speex spell sql sqlite sqlite3 sse sse2 sse3 ssl ssse3 subversion svg sysfs system-sqlite t1lib taglib tcpd theora threads tidy tiff timidity tk truetype tta udev unicode upnp usb v4l v4l2 vaapi vcd vhosts vim vim-syntax vorbis wav wavepack wicd wifi wma wmf wmp wxwidgets wxwindows x264 x86emu xattr xcb xcomposite xetex xforms xft xine xinerama xml xmmp xorg xosd xrandr xsl xv xvid yahoo zip zlib" ALSA_CARDS="hda-intel" 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 cgi cgid 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 proxy_http proxy" APACHE2_MPMS="worker" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" DRACUT_MODULES="plymouth lvm gensplash crypt 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" GRUB_PLATFORMS="coreboot efi-32 efi-64 multiboot pc" INPUT_DEVICES="evdev joystick keyboard mouse synaptics wacom" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en ja zh zh_CN zh_TW en_US en_GB" NETBEANS_MODULES="cnd php mobility websvccommon apisupport java ide harness nb dlight enterprise profiler" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="intel i965 vesa vga fbdev v4l" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Mathieu Z 2012-02-17 11:07:43 UTC]

Created attachment 302253 [details]
build.log

[Comment 2 Justin Lecher (RETIRED) 2012-02-17 11:24:28 UTC]

Please make sure that you have blas-reference and lapack-reference from the sci overlay. And that eselect blas and eselect lapack both are set correctly.

[Comment 3 Mathieu Z 2012-02-17 11:38:32 UTC]

(In reply to comment #2)
> Please make sure that you have blas-reference and lapack-reference from the sci
> overlay. And that eselect blas and eselect lapack both are set correctly.

Of course:

# eselect blas show
reference
# eselect lapack show
reference

# eix -I reference
[I] sci-libs/blas-reference
     Available versions:  20070226 (~)20070226-r1 (~)20070226-r2 (~)20110418[1] (~)20111123[1] (~)20120215[1] **99999999[1] {doc}
     Installed versions:  20120215[1](04:10:29 PM 02/16/2012)(-static-libs -test)
     Homepage:            http://www.netlib.org/blas/
     Description:         Basic Linear Algebra Subprograms F77 reference implementations

[I] sci-libs/lapack-reference
     Available versions:  3.1.1-r1 (~)3.2.1 (~)3.2.1-r1 (~)3.3.1-r1[1] (~)3.4.0[1] (~)3.4.0_p20120215[1] **9999[1] {doc}
     Installed versions:  3.4.0_p20120215[1](03:10:52 AM 02/17/2012)(xblas -static-libs -test)
     Homepage:            http://www.netlib.org/lapack/index.html
     Description:         FORTRAN reference implementation of LAPACK Linear Algebra PACKage

[1] "science" /var/lib/layman/science

[Comment 4 Mathieu Z 2012-02-17 11:40:47 UTC]

Also:
# cat /usr/lib64/pkgconfig/blas.pc
prefix=/usr
libdir=/usr/lib64

Name: blas
Description: Basic Linear Algebra Subprograms F77 reference implementations
Version: 
URL: http://www.netlib.org/blas/
Libs: -L/usr/lib64 -lblas
Libs.private: -lm

but /usr/lib64/libblas.so is not installed. Should change to -lrefblas??

[Comment 5 Justin Lecher (RETIRED) 2012-02-17 11:42:37 UTC]

please do
eselect blas set reference
again.

[Comment 6 Mathieu Z 2012-02-17 11:51:04 UTC]

(In reply to comment #5)
> please do
> eselect blas set reference
> again.

Already did. sci-libs/blas-reference-20120215 installs these files:
# qlist blas-reference
/etc/env.d/alternatives/blas/reference/usr/lib64/pkgconfig/blas.pc
/etc/env.d/alternatives/blas/reference/_importance
/usr/lib64/librefblas.so
/usr/lib64/pkgconfig/refblas.pc

but refblas.pc has -lblas in it while it should be -lrefblas to reference librefblas.so.

[Comment 7 Justin Lecher (RETIRED) 2012-02-17 12:12:19 UTC]

which eselect version do you have installed?

[Comment 8 Mathieu Z 2012-02-17 12:17:09 UTC]

(In reply to comment #7)
> which eselect version do you have installed?

# eix -eI eselect
[I] app-admin/eselect
     Available versions:  1.2.15 1.2.18 (~)1.3 (~)1.3.1 (~)1.3.1-r1[1] **9999 {doc}
     Installed versions:  1.3.1-r1[1](10:58:26 PM 02/13/2012)(-doc)
     Homepage:            http://www.gentoo.org/proj/en/eselect/
     Description:         Gentoo's multi-purpose configuration and management tool

[1] "science" /var/lib/layman/science

[Comment 9 Justin Lecher (RETIRED) 2012-02-17 12:23:24 UTC]

okay I can reproduce it here

[Comment 10 Justin Lecher (RETIRED) 2012-02-20 10:03:14 UTC]

Fixed in -r1