Works fine if eselected reference implementations of blas and lapack. Reproducible: Always Steps to Reproduce: 1. emerge -1 sci-libs/atlas 2. eselect blas set atlas 3. eselect lapack set atlas 4. emerge -1 dev-python/numpy Actual Results: Build fails because ld can not find -lblas. Expected Results: Successful emerge. Portage 2.1.10.24 (default/linux/amd64/10.0/desktop/gnome, gcc-4.6.1, glibc-2.13-r4, 3.0.6-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.0.6-gentoo-x86_64-Intel-R-_Core-TM-_i7-2630QM_CPU_@_2.00GHz-with-gentoo-2.1 Timestamp of tree: Sun, 09 Oct 2011 08:15:01 +0000 app-shells/bash: 4.2_p10 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.6.7-r2, 2.7.2-r3, 3.1.4-r3, 3.2.2 dev-util/cmake: 2.8.5-r2 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1 sys-apps/openrc: 0.9.3-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-r1 sys-devel/gcc: 4.4.6-r1, 4.5.3-r1, 4.6.1-r1 sys-devel/gcc-config: 1.4.1-r1 sys-devel/libtool: 2.4-r3 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 2.6.39 (virtual/os-headers) sys-libs/glibc: 2.13-r4 Repositories: gentoo x11 science x-portage ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe -ggdb" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/lib/hsqldb" 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 -O2 -pipe -ggdb" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="" FEATURES="assume-digests binpkg-logs compress-build-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch parallel-install protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="" GENTOO_MIRRORS="ftp://trumpetti.atm.tut.fi/gentoo/ http://trumpetti.atm.tut.fi/gentoo/ http://gentoo.tups.lv/source/ " LANG="lv_LV.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="lv en" MAKEOPTS="-j9 -s" 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/science /usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="X a52 aac acl acpi alsa amd64 avx bash-completion berkdb bluetooth branding bzip2 cairo cdda cdio cdr cjk cleartype cli consolekit cracklib crypt cups cxx dbus dirac djvu dri dts dvd dvdr eds emboss encode evo exif fam ffmpeg fftw firefox flac fontconfig fortran gdbm gdu gif gnome gnome-keyring gphoto2 gpm gsm gstreamer gtk iconv idn ipv6 jpeg kate lcms ldap libcaca libnotify live mad matroska mmx mng modules mp3 mp4 mpeg mtp mudflap multilib musepack nautilus ncurses networkmanager nls nptl nptlonly ogg openexr opengl openmp pam pango pcre pdf png policykit ppds pppd pulseaudio qt3support qt4 raw readline schroedinger sdl session smp speex spell sse sse2 sse4_1 ssl ssse3 startup-notification svg sysfs system-sqlite tcpd theora tiff truetype udev unicode usb v4l v4l2 vaapi vorbis wmf x264 xcb xetex xml xmp xorg xpm xulrunner xv xvid xvmc zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci 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 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" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" FOO2ZJS_DEVICES="hp1018" 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="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="lv en" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="fbdev nvidia i965 intel 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, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= dev-python/numpy-1.6.1-r1 was built with the following: USE="lapack (multilib) -doc -test" LDFLAGS="-Wl,-O1 -Wl,--as-needed -shared" [I] sci-libs/atlas [1] Available versions: (~)3.8.4 (~)3.9.46 (~)3.9.47 (~)3.9.49 {doc fortran lapack static-libs threads} Installed versions: 3.9.49(17:13:46 2011.10.09.)(fortran lapack threads -doc -static-libs) Homepage: http://math-atlas.sourceforge.net/ Description: Automatically Tuned Linear Algebra Software [1] "science" /var/lib/layman/science Available providers for blas: [1] atlas * [2] atlas-threads [3] reference Available providers for lapack: [1] atlas * [2] atlas-threads [3] reference
Created attachment 289357 [details] Compressed build log # pkg-config --libs blas -lf77blas -lm -latlas # pkg-config --libs lapack -latllapack -lf77blas -lm -latlas -lgslcblas
Created attachment 289473 [details, diff] A better atlas patch Remove atlas config functions from the list of supported configs. We are interested in blas and lapack libraries anyway, and those can be properly found. Tested with reference and atlas implementations. Both works now.
Created attachment 289475 [details, diff] numpy-1.6.1-r1.ebuild patch
(In reply to comment #3) > Created attachment 289475 [details, diff] > numpy-1.6.1-r1.ebuild patch I confirm that this version compiles when atlas is eselected.
It works for me as well (on a Gentoo Prefix), thanks for the patches!
+ 27 Oct 2011; Justin Lecher <jlec@gentoo.org> numpy-1.6.1-r1.ebuild, + files/numpy-1.6.1-atlas.patch: + Included fixes for atlas, #386531; thanks My Th for the patch +
