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Bug 543560 - =sci-libs/scikits_learn-0.15.2 needs cblas beeing set (cblas alternatives are not set after emerge)
Summary: =sci-libs/scikits_learn-0.15.2 needs cblas beeing set (cblas alternatives are...
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: x86 Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2015-03-16 23:47 UTC by mike
Modified: 2018-09-09 16:48 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments

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Description mike 2015-03-16 23:47:11 UTC
Compilation sci-libs/scikits_learn fails because cblas was not set. Setting it via "eselect cblas set 1" worked for me.

Reproducible: Always

Steps to Reproduce:
1. emerge =sci-libs/scikits_learn-0.15.2 (without cblas beeing set, check via eselect cblas list)

Actual Results:  
Compilation fails.

Expected Results:  
Compilation succeeds

Portage 2.2.14 (python 3.3.5-final-0, default/linux/x86/13.0, gcc-4.8.3, glibc-2.19-r1, 3.18.7-gentoo i686)
=================================================================
System uname: Linux-3.18.7-gentoo-i686-Intel-R-_Core-TM-2_Duo_CPU_L9400_@_1.86GHz-with-gentoo-2.2
KiB Mem:     6109668 total,   2783764 free
KiB Swap:    5121020 total,   5121020 free
Timestamp of tree: Mon, 16 Mar 2015 16:15:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
ccache version 3.1.9 [enabled]
app-shells/bash:          4.2_p53
dev-java/java-config:     2.2.0
dev-lang/perl:            5.20.1-r4
dev-lang/python:          2.7.9-r1, 3.3.5-r1, 3.4.1
dev-util/ccache:          3.1.9-r4
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.13.11
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.10.3-r1, 1.11.6-r1, 1.13.4
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.4
sys-devel/make:           4.1-r1
sys-kernel/linux-headers: 3.16 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo tud_overlay
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="* -@EULA"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=i686 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib/libreoffice/program/sofficerc /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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=i686 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -march=i686 -pipe"
FEATURES="assume-digests binpkg-logs ccache config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -march=i686 -pipe"
GENTOO_MIRRORS="http://de-mirror.org/gentoo/"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-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="/usr/local/portage"
SYNC="rsync://rsync1.de.gentoo.org/gentoo-portage"
USE="X acl acpi alsa bash-completion berkdb bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 jpeg jpeg2k jpg keymap libav modules ncurses networkmanager nptl opengl openmp pam pcre png qt3support readline sdl session sse sse2 ssl tcpd threads unicode v4l x86 xinerama zlib" ABI_X86="32" 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" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="sse sse2" 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 ublox ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="intel i915" 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, USE_PYTHON
Comment 1 mike 2015-03-16 23:49:58 UTC
I'm not sure if calling "eselect set..." automatically on compiling is the default behaviour if there is nothing set but there was no information about to set it.
Comment 2 Michael Palimaka (kensington) gentoo-dev 2015-03-17 12:24:34 UTC
Please attach the build log.
Comment 3 mike 2015-03-17 15:52:08 UTC
(In reply to Michael Palimaka (kensington) from comment #2)
> Please attach the build log.

Sorry, it was allready removed after successfull emerge and now cblas can't be unset to reproduce it.
Comment 4 Andrew Savchenko gentoo-dev 2015-03-25 22:23:59 UTC
If no cblas implementation was selected, this is normal than package fails to build. What is not normal, that cblas was installed, but no implementation was selected.

Mike, what cblas implementations do you have installed?
Comment 5 mike 2015-03-26 00:31:15 UTC
(In reply to Andrew Savchenko from comment #4)
> Mike, what cblas implementations do you have installed?

I've got:

[I] app-admin/eselect-cblas
     Available versions:  0.1
     Installed versions:  0.1(17:03:21 18.03.2014)
     Homepage:            http://www.gentoo.org/proj/en/eselect/
     Description:         C-language BLAS module for eselect

[I] virtual/cblas
     Available versions:  1.0
     Installed versions:  1.0(16:32:15 18.03.2014)
     Description:         Virtual for BLAS C implementation
Comment 6 Andrew Savchenko gentoo-dev 2015-03-26 06:20:16 UTC
That's only virtual and eselect module. Please show `eselect cblas list` output. You should have something like gsl or mkl there (full list is in the virtual/cblas ebuild).
Comment 7 mike 2015-03-26 15:14:56 UTC
(In reply to Andrew Savchenko from comment #6)
> That's only virtual and eselect module. Please show `eselect cblas list`
> output. You should have something like gsl or mkl there (full list is in the
> virtual/cblas ebuild).

Installed CBLAS for library directory lib
  [1]   gsl *
Comment 8 Roman Yurchak 2018-09-08 08:03:20 UTC
scikit-learn 0.15.2 is quite outdated, it is currently masked in Gentoo, so I think this bug can be closed.
Comment 9 Amy Liffey gentoo-dev 2018-09-09 16:48:43 UTC
Thanks