numpy-1.6.1-r1 fails to compile but numpy-1.6.1 compiles with no problem. ------------------------------------------------------------ emerge -pqv =dev-python/numpy-1.6.1-r1 [ebuild U ] dev-python/numpy-1.6.1-r1 [1.6.1] USE="lapack -doc -test" emerge --info =dev-python/numpy-1.6.1-r1 Portage 2.2.0_alpha64 (default/linux/x86/10.0, gcc-4.5.3, glibc-2.13-r4, 3.0.6-gentoo-ole i686) ================================================================= System Settings ================================================================= System uname: Linux-3.0.6-gentoo-ole-i686-Intel-R-_Core-TM-2_Duo_CPU_E6550_@_2.33GHz-with-gentoo-2.1 Timestamp of tree: Sun, 09 Oct 2011 12:45:01 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] ccache version 3.1.6 [enabled] app-shells/bash: 4.2_p10 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2-r3, 3.2.2 dev-util/ccache: 3.1.6 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: 1.4_p6-r1, 1.5, 1.6.3, 1.7.9-r2, 1.8.5-r3, 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 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 kde-sunset vmware dev-jokey perl-experimental science sunrise gnome my-overlays Installed sets: @kde-3.5, @kde-4, @system ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="*" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=prescott -O2 -pipe -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /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/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=prescott -O2 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs ccache distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="ftp://files.gentoo.gr/ ftp://gentoo.arcticnetwork.ca/pub/gentoo/" LANG="el_GR.ISO-8859-7" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en el" MAKEOPTS="-j11" PKGDIR="/usr/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="/usr/portage/local/layman/kde-sunset /usr/portage/local/layman/vmware /usr/portage/local/layman/jokey /usr/portage/local/layman/perl-experimental /usr/portage/local/layman/science /usr/portage/local/layman/sunrise /usr/portage/local/layman/gnome /usr/portage/local" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="X aac acl alsa arts avahi bash-completion berkdb bzip2 cli cracklib cups curl cxx dbus dri dvd fam ffmpeg flac fontconfig fortran gdbm gif gpm gtk iconv imagemagick introspection java jpeg kde mad mmx mmxext modules mono mp3 mplayer mudflap mysql ncurses nls npp nptl nptlonly nsplugin ogg opengl opengli openmp oss pam pcre pdf perl png pppd python qt3support rdesktop readline samba session slang spell sse sse2 sse3 ssl ssse3 svg sysfs tcpd tetex tiff tk truetype udev unicode vorbis win32codecs x86 xorg xpm xulrunner xv xvid zeroconf 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 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" 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="en el" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby18" SANE_BACKENDS="plustek" USERLAND="GNU" VIDEO_CARDS="nvidia" 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 Reproducible: Always
Created attachment 289355 [details] The build log
Also note that without the "lapack" use flag: USE="-lapack" emerge -1va =dev-python/numpy-1.6.1-r1 compilation succeeds.
standard questions for that kind of failure: eselect blas list eselect cblas list eselect lapack list If atlas is used, version used with useflags.
(In reply to comment #3) ========================================================== ~# eselect cblas list Available providers for cblas: [1] atlas [2] gsl [3] reference * ~# eselect blas list Available providers for blas: [1] atlas [2] reference * ~# eselect lapack list Available providers for lapack: [1] atlas [2] reference * ~# equery u sci-libs/atlas * Found these USE flags for sci-libs/atlas-3.9.49: U I - - doc : Adds extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally + + fortran : Adds support for fortran (formerly f77) + + lapack : Adds support for the virtual/lapack numerical library - - static-libs : Build static libraries - - threads : Adds threads support for various packages. Usually pthreads ======================================================= Note that if all the above are set to 'atlas' numpy still fails to compile
There is a bunch of bug about numpy/scipy not working for some people with the new blas/lapack stack from the science overlay. More accurately new users. I have migrated ages ago and I am fine and so are other. Looking at your build log you have blas being detected when it shouldn't. Would you have broken links to libblas and libcblas in /usr/lib/?
(In reply to comment #5) > Would you have broken links to libblas and libcblas in /usr/lib/? I found broken links as you said, deleted them and numpy compiled. Thanks for the tip.
Thanks for confirming it. I think checking for these need to be part of some migration documentation, it may well be the source of the other bugs.
