sci-mathematics/octave both versions 3.4.3-r1 and 3.6.3 fail compilation during linking stage while trying to link with ATLAS libraries. ATLAS libraries are currently masked, so I unmerged them and installed blas-reference and lapack-reference. Then I wanted to emerge octave, but it tries to link with atlas and fails with: ld: cannot find -latlas Reproducible: Always thor strazce # emerge --info Portage 2.2.0_alpha158 (default/linux/amd64/10.0/desktop/gnome, gcc-4.6.3, glibc-2.15-r3, 3.6.11-gentoo-sh x86_64) ================================================================= System uname: Linux-3.6.11-gentoo-sh-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9450_@_2.66GHz-with-gentoo-2.1 KiB Mem: 8169860 total, 342200 free KiB Swap: 2191356 total, 2071252 free Timestamp of tree: Mon, 21 Jan 2013 13:00:01 +0000 ld GNU ld (GNU Binutils) 2.22 app-shells/bash: 4.2_p37 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.7.3-r2, 3.2.3 dev-util/cmake: 2.8.9 dev-util/pkgconfig: 0.27.1 sys-apps/baselayout: 2.1-r1 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.6.3, 4.7.2 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.6 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: gentoo local-repo lcd-filtering science forked-daapd calculate proaudio sunrise steam-overlay Installed sets: @system ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA ut2003 dlj-1.1 googleearth AdobeFlash-10.3 Intel-SDP Oracle-BCLA-JavaSE PUEL google-chrome" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=core2 -msse4.1 -O2 -pipe -ggdb" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/ext-active/ /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=core2 -msse4.1 -O2 -pipe -ggdb" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="en_GB.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" 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="/home/portage-tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage /usr/local/overlays/lcd-filtering /usr/local/overlays/science /usr/local/overlays/forked-daapd /usr/local/overlays/calculate /usr/local/overlays/pro-audio /usr/local/overlays/sunrise /usr/local/overlays/steam" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac aacplus aalib acl acpi alsa amd64 amr ass bash-completion berkdb bluetooth branding bzip2 cairo cdda cddb cdr cleartype cli colord consolekit cracklib crypt css cups curl cxx dbus dga dirac divx doc dri dssi dts dv dvd dvdr dvdread eds emboss encode evo exif expat faac faad fam fbcon ffmpeg fftw firefox flac fontconfig fortran fuse gconf gd gdbm gif gimp glade glib gmp gnome gnome-keyring gnome-online-accounts gnutls gphoto2 gpm gsm gstreamer gtk gtkhtml hdf5 iconv idn ieee1394 imagemagick imlib introspection ios ipv6 jack java java6 jbig jpeg jpeg2k ladspa lame lapack lcms libcaca libedit libffi libnotify libsamplerate lzma lzo mad midi mikmod mmap mms mmx mng mod modplug modules mono mp3 mp4 mpeg mplayer mudflap multilib musepack natspec nautilus ncurses newspr nls nptl nsplugin numpy offensive ogg openal opencore-amr openexr opengl openmp pam pango pch pcre pdf perl pic png policykit ppds pulseaudio python qt3support quicktime raw readline samba sasl schroedinger sdl session smp sndfile socialweb speex spell sse sse2 sse3 ssl ssse3 startup-notification svg t1lib tcl tcpd theora threads tiff tk truetype tta twolame udev udisks unicode upnp-av upower usb v4l v4l2 vcd vdpau vim-syntax vorbis vpx wavpack webp wmf wxwidgets x264 xcb xinerama xml xmp xpm xulrunner xv xvid xvmc yv12 zlib" ALSA_CARDS="emu10k1" ALSA_PCM_PLUGINS="*" APACHE2_MODULES="*" APACHE2_MPMS="prefork" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="*" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" DVB_CARDS="usb-af9015 usb-dib0700" 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="evdev joystick keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="*" LINGUAS="en_GB en_US en cs_CZ cs" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="*" QEMU_USER_TARGETS="*" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nvidia 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON [ebuild N ~] sci-mathematics/octave-3.6.3 USE="X curl doc fftw glpk hdf5 imagemagick opengl qhull qrupdate readline sparse zlib -gnuplot -postscript -static-libs" 0 kB
Created attachment 336348 [details] build.log Attached the build log - even the last build command alone is too long to fit in comment.
did you eselect the new implementations?
Yes, I did that after I unmerged ATLAS (using emerge -C): thor strazce # eselect lapack list Installed LAPACK for library directory lib64 [1] mkl-gfortran [2] mkl-gfortran-int64 [3] mkl-gfortran-threads [4] mkl-gfortran-threads-int64 [5] reference * thor strazce # eselect blas list Installed BLAS for library directory lib64 [1] mkl-gfortran [2] mkl-gfortran-int64 [3] mkl-gfortran-threads [4] mkl-gfortran-threads-int64 [5] reference *
and cblas?
Please try a revdep-rebuild. It seems your system has some broken links.
Thank you. revdep-rebuild fixed it. I was relying on emerge @preserved-rebuild, it didn't occur to me, it wouldn't work in this case.
