-
Bug
-
Resolution: Fixed
-
Minor
-
None
-
None
-
- emerge --info numpy
Portage 2.3.6-r7 (funtoo/1.0/linux-gnu/arch/x86-64bit, gcc-4.8.2, glibc-2.18, 3.14.0-gentoo x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-3.14.0-gentoo-x86_64-AMD_FX-tm-8350_Eight-Core_Processor-with-gentoo-2.2.0
KiB Mem: 16383164 total, 2760692 free
KiB Swap: 39078612 total, 38381344 free
Timestamp of tree: Sat, 10 May 2014 10:45:01 +0000
ld GNU ld (GNU Binutils) 2.22
app-shells/bash: 4.2_p45-r1
dev-java/java-config: 2.2.0-r1000
dev-lang/python: 2.7.6-r1001, 3.2.5-r1000, 3.3.5-r1000
dev-util/cmake: 2.8.12.2-r1
sys-apps/baselayout: 2.2.0-r6
sys-apps/openrc: 0.12.3-r1
sys-apps/sandbox: 2.6-r2
sys-devel/autoconf: 2.13, 2.69
sys-devel/automake: 1.11.6, 1.12.6, 1.13.4
sys-devel/binutils: 2.22-r1
sys-devel/gcc: 4.6.4-r2, 4.8.2-r2
sys-devel/gcc-config: 1.8
sys-devel/libtool: 2.4.2
sys-devel/make: 4.0-r1
sys-kernel/linux-headers: 3.13 (virtual/os-headers)
sys-libs/glibc: 2.18
Repositories: gentoo science
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA @FREE"
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 /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /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 /etc/udev/rules.d"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="-j3 --load-average=8"
FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms split-log splitdebug strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://www.mirrorservice.org/sites/www.ibiblio.org/gentoo/"
LANG="en_GB.utf8"
LDFLAGS="Wl,-O1 -Wl,sort-common -Wl,-as-needed"
LINGUAS="en en_GB eo"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/science"
SYNC="git://github.com/funtoo/ports-2012.git"
SYNC_USER="root"
USE="X acl alsa amd64 amr apng aspell attica avahi avx bash-completion berkdb bmp boost bs2b bzip2 c+0x c+11 cairo caps cdda cddb cdr celt cjk colord consolekit corefonts cracklib crypt cups curl cxx dbus device-mapper dga directfb djvu dri dtmf dv dvd dvdr dvdread emf epub evo exif fam fbcon ffmpeg fftw flac flash fontconfig gdbm gif gimp git glamor gnome gnome-keyring gnuplot gpg gpm gps gsm gstreamer gtk gtk3 h323 hdf5 iconv icu idn ilbc imagemagick inotify introspection ipv6 ivr jabber jingle jpeg jpeg2k kde kipi kontact lame lapack latex lcms libnotify libsamplerate libsecret lm_sensors lzma mad matroska metric mjpeg mmx mmxext mng modules mp3 mpeg mpeg2 mplayer msn mtp mudflap multilib musicbrainz nautilus ncurses networkmanager nls nptl nsplugin ntp ogg openal opencl openexr opengl openmp openvg opus osmesa otr pam pch pcre pdf pgo plasma plotutils png policykit postscript pppd prison pulseaudio pygments python qalculate qt4 quicktime quvi raw readline resolvconf samba schroedinger sdl semantic-desktop sip sipim smp speex spell srtp sse sse2 sse4_1 ssl ssse3 startup-notification svg taglib tcpd theora threads tiff truetype udev udisks unicode upnp upower vorbis vpx wav wavpack webm webp win32codecs wmf x264 xattr xcomposite xinerama xml xmp xpm xv xvid xvmc yahoo zeroconf zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel ice1724 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 auth_digest authn_alias authn_anon authn_default authn_file authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir env expires filter headers include info log_config log_forensic logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" APACHE2_MPMS="worker" 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" DRACUT_MODULES="crypt zfs" ELIBC="glibc" GPSD_PROTOCOLS="garmin garmintxt" GRUB_PLATFORMS="coreboot efi-64 pc" INPUT_DEVICES="evdev synaptics keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console nlpsolver pdfimport wiki-publisher presenter-minimizer" LINGUAS="en en_GB eo" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_ABIS="2.7 3.3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="radeon r100 r200 r300 r600 radeonsi 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, SYNC_UMASK
=================================================================
Package Settings
=================================================================dev-python/numpy-1.8.1-r1000 was built with the following:
USE="doc lapack test" PYTHON_ABIS="2.7 3.3 -2.6 -3.1 -3.2 -3.4 -3.5" PYTHON_TARGETS="python2_7 python3_3"
LDFLAGS="Wl,-O1 -Wl,sort-common -Wl,-as-needed -shared"- eselect blas list
Available providers for blas:
[1] atlas
[2] atlas-threads *
[3] reference
- eselect lapack list
Available providers for lapack:
[1] atlas
[2] atlas-threads *
[3] reference
emerge --info numpy Portage 2.3.6-r7 (funtoo/1.0/linux-gnu/arch/x86-64bit, gcc-4.8.2, glibc-2.18, 3.14.0-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.14.0-gentoo-x86_64-AMD_FX-tm-8350_Eight-Core_Processor-with-gentoo-2.2.0 KiB Mem: 16383164 total, 2760692 free KiB Swap: 39078612 total, 38381344 free Timestamp of tree: Sat, 10 May 2014 10:45:01 +0000 ld GNU ld (GNU Binutils) 2.22 app-shells/bash: 4.2_p45-r1 dev-java/java-config: 2.2.0-r1000 dev-lang/python: 2.7.6-r1001, 3.2.5-r1000, 3.3.5-r1000 dev-util/cmake: 2.8.12.2-r1 sys-apps/baselayout: 2.2.0-r6 sys-apps/openrc: 0.12.3-r1 sys-apps/sandbox: 2.6-r2 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.11.6, 1.12.6, 1.13.4 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.6.4-r2, 4.8.2-r2 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 4.0-r1 sys-kernel/linux-headers: 3.13 (virtual/os-headers) sys-libs/glibc: 2.18 Repositories: gentoo science ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA @FREE" 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 /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /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 /etc/udev/rules.d" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="-j3 --load-average=8" FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms split-log splitdebug strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv xattr" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="http://www.mirrorservice.org/sites/www.ibiblio.org/gentoo/" LANG="en_GB.utf8" LDFLAGS=" Wl,-O1 -Wl, sort-common -Wl, -as-needed" LINGUAS="en en_GB eo" MAKEOPTS="-j4" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/science" SYNC="git://github.com/funtoo/ports-2012.git" SYNC_USER="root" USE="X acl alsa amd64 amr apng aspell attica avahi avx bash-completion berkdb bmp boost bs2b bzip2 c+ 0x c +11 cairo caps cdda cddb cdr celt cjk colord consolekit corefonts cracklib crypt cups curl cxx dbus device-mapper dga directfb djvu dri dtmf dv dvd dvdr dvdread emf epub evo exif fam fbcon ffmpeg fftw flac flash fontconfig gdbm gif gimp git glamor gnome gnome-keyring gnuplot gpg gpm gps gsm gstreamer gtk gtk3 h323 hdf5 iconv icu idn ilbc imagemagick inotify introspection ipv6 ivr jabber jingle jpeg jpeg2k kde kipi kontact lame lapack latex lcms libnotify libsamplerate libsecret lm_sensors lzma mad matroska metric mjpeg mmx mmxext mng modules mp3 mpeg mpeg2 mplayer msn mtp mudflap multilib musicbrainz nautilus ncurses networkmanager nls nptl nsplugin ntp ogg openal opencl openexr opengl openmp openvg opus osmesa otr pam pch pcre pdf pgo plasma plotutils png policykit postscript pppd prison pulseaudio pygments python qalculate qt4 quicktime quvi raw readline resolvconf samba schroedinger sdl semantic-desktop sip sipim smp speex spell srtp sse sse2 sse4_1 ssl ssse3 startup-notification svg taglib tcpd theora threads tiff truetype udev udisks unicode upnp upower vorbis vpx wav wavpack webm webp win32codecs wmf x264 xattr xcomposite xinerama xml xmp xpm xv xvid xvmc yahoo zeroconf zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel ice1724 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 auth_digest authn_alias authn_anon authn_default authn_file authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir env expires filter headers include info log_config log_forensic logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" APACHE2_MPMS="worker" 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" DRACUT_MODULES="crypt zfs" ELIBC="glibc" GPSD_PROTOCOLS="garmin garmintxt" GRUB_PLATFORMS="coreboot efi-64 pc" INPUT_DEVICES="evdev synaptics keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console nlpsolver pdfimport wiki-publisher presenter-minimizer" LINGUAS="en en_GB eo" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_ABIS="2.7 3.3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="radeon r100 r200 r300 r600 radeonsi 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, SYNC_UMASK ================================================================= Package Settings ================================================================= dev-python/numpy-1.8.1-r1000 was built with the following: USE="doc lapack test" PYTHON_ABIS="2.7 3.3 -2.6 -3.1 -3.2 -3.4 -3.5" PYTHON_TARGETS="python2_7 python3_3" LDFLAGS=" Wl,-O1 -Wl, sort-common -Wl, -as-needed -shared" eselect blas list Available providers for blas: [1] atlas [2] atlas-threads * [3] reference eselect lapack list Available providers for lapack: [1] atlas [2] atlas-threads * [3] reference - emerge --info numpy
I have sci-libs/atlas-3.10.1-r2 installed from the gentoo-science overlay. If I build numpy (dev-python/numpy-1.8.1-r1000) by running `emerge numpy`, the build log contains "UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found." (see the attached numpy-1.8.1-r1000.log) but if I do `tar -xf /usr/portage/distfiles/numpy-1.8.1.tar.gz; cd numpy-1.8.1; python setup.py build` then ATLAS is found (see my_numpy.log)
N.B. I also get this error when building sci-libs/scipy, but I think scipy gets its information about optimised BLAS from numpy/distutils/site.cfg
