I switch to the atlas implementation of the science overlay. When running revdep-rebuild, pysparse failed to build, because blas/lapack was missing : /usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -llapack /usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lblas Emerging others libriries such as numpy, scipy works just fine. Reproducible: Always Steps to Reproduce: 1. switch to the atlas implementation 2. emerge pysparse Actual Results: Emerge failed Expected Results: The installation should proceed without errors emerge --info Portage 2.1.11.62 (default/linux/amd64/13.0, gcc-4.6.3, glibc-2.15-r3, 3.7.4-gentoo x86_64) ================================================================= System uname: Linux-3.7.4-gentoo-x86_64-Intel-R-_Core-TM-_i7-3612QM_CPU_@_2.10GHz-with-gentoo-2.2 KiB Mem: 8073004 total, 2492236 free KiB Swap: 3903788 total, 3903788 free Timestamp of tree: Sun, 05 May 2013 14:30:01 +0000 ld GNU ld (GNU Binutils) 2.22 app-shells/bash: 4.2_p45 dev-lang/python: 2.7.5_pre20130505::progress, 3.2.4-r1000::progress dev-util/cmake: 2.8.10.2-r2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.11.6, 1.12.6 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.6.3 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.9 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: gentoo location: /usr/portage sync: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 science location: /var/lib/layman/science masters: gentoo priority: 0 gentoo-haskell location: /var/lib/layman/haskell masters: gentoo priority: 1 sage-on-gentoo location: /var/lib/layman/sage-on-gentoo masters: gentoo priority: 2 progress location: /var/lib/layman/progress masters: gentoo priority: 3 ABI="amd64" ABI_X86="64" ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" ACCEPT_PROPERTIES="*" 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="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" ARCH="amd64" AUTOCLEAN="yes" BOOTSTRAP_USE="cxx unicode python_targets_python3_2 python_targets_python2_7 multilib" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -fomit-frame-pointer -march=native" CFLAGS_amd64="-m64" CFLAGS_x32="-mx32" CFLAGS_x86="-m32" CHOST="x86_64-pc-linux-gnu" CHOST_amd64="x86_64-pc-linux-gnu" CHOST_x32="x86_64-pc-linux-gnux32" CHOST_x86="i686-pc-linux-gnu" CLEAN_DELAY="5" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" COLLISION_IGNORE="/lib/modules/* *.py[co] *$py.class" COLORTERM="rxvt" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /usr/share/polkit-1/actions" CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /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 -pipe -fomit-frame-pointer -march=native" DEFAULT_ABI="amd64" DISPLAY=":0.0" DISTDIR="/usr/portage/distfiles" DRACUT_MODULES="crypt" EDITOR="/usr/bin/vim" ELIBC="glibc" EMERGE_DEFAULT_OPTS="--ask --verbose" EMERGE_WARNING_DELAY="10" EPREFIX="" EROOT="/" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FETCHCOMMAND="wget -t 3 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}"" FETCHCOMMAND_RSYNC="rsync -avP "${URI}" "${DISTDIR}/${FILE}"" FETCHCOMMAND_SFTP="bash -c "x=\${2#sftp://} ; host=\${x%%/*} ; port=\${host##*:} ; host=\${host%:*} ; [[ \${host} = \${port} ]] && port=22 ; exec sftp -P \${port} \"\${host}:/\${x#*/}\" \"\$1\"" sftp "${DISTDIR}/${FILE}" "${URI}"" FETCHCOMMAND_SSH="bash -c "x=\${2#ssh://} ; host=\${x%%/*} ; port=\${host##*:} ; host=\${host%:*} ; [[ \${host} = \${port} ]] && port=22 ; exec rsync --rsh=\"ssh -p\${port}\" -avP \"\${host}:/\${x#*/}\" \"\$1\"" rsync "${DISTDIR}/${FILE}" "${URI}"" FFLAGS="-O2 -pipe" FLTK_DOCDIR="/usr/share/doc/fltk-1.3.0-r1/html" GCC_SPECS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" 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" GRUB_PLATFORMS="" GSETTINGS_BACKEND="gconf" HG="/usr/bin/hg" HOME="/root" INFOPATH="/usr/share/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.6.3/info:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.22/info" INPUT_DEVICES="evdev synaptics keyboard mouse" IUSE_IMPLICIT="prefix" KDE_IS_PRELINKED="1" KERNEL="linux" LANG="fr_FR.UTF-8" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LC_COLLATE="C" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LDFLAGS_amd64="-m elf_x86_64" LDFLAGS_x32="-m elf32_x86_64" LDFLAGS_x86="-m elf_i386" LESS="-R -M --shift 5" LESSOPEN="|lesspipe %s" LIBDIR_amd64="lib64" LIBDIR_amd64_fbsd="lib64" LIBDIR_n32="lib32" LIBDIR_n64="lib64" LIBDIR_o32="lib" LIBDIR_ppc="lib32" LIBDIR_ppc64="lib64" LIBDIR_s390="lib32" LIBDIR_s390x="lib64" LIBDIR_sparc32="lib32" LIBDIR_sparc64="lib64" LIBDIR_x32="libx32" LIBDIR_x86="lib32" LIBDIR_x86_fbsd="lib32" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="fr en" LOGNAME="root" MAKEOPTS="-j8" MANPATH="/usr/local/share/man:/usr/share/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.6.3/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.22/man" MULTILIB_ABIS="amd64 x86" MULTILIB_STRICT_DENY="64-bit.*shared object" MULTILIB_STRICT_DIRS="/lib32 /lib /usr/lib32 /usr/lib /usr/kde/*/lib32 /usr/kde/*/lib /usr/qt/*/lib32 /usr/qt/*/lib /usr/X11R6/lib32 /usr/X11R6/lib" MULTILIB_STRICT_EXEMPT="(perl5|gcc|gcc-lib|binutils|eclipse-3|debug|portage|udev)" MULTIOSDIRS="../lib64:../lib32" NETBEANS="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" OLDPWD="/root" OPENGL_PROFILE="xorg-x11" PAGER="/usr/bin/less" PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.6.3" PHP_TARGETS="php5-3" PKGDIR="/usr/portage/packages" PORTAGE_ARCHLIST="ppc sparc64-freebsd ppc-openbsd x86-openbsd ppc64 x86-winnt x86-fbsd ppc-aix alpha arm x86-freebsd s390 amd64 arm-linux x86-macos x64-openbsd ia64-hpux hppa x86-netbsd ppc64-linux x86-cygwin amd64-linux ia64-linux x86 sparc-solaris x64-freebsd sparc64-solaris x86-linux x64-macos sparc m68k-mint ia64 mips ppc-macos x86-interix hppa-hpux amd64-fbsd x64-solaris m68k sh x86-solaris sparc-fbsd" PORTAGE_BIN_PATH="/usr/lib64/portage/bin" PORTAGE_COMPRESS_EXCLUDE_SUFFIXES="css gif htm[l]? jp[e]?g js pdf png" PORTAGE_CONFIGROOT="/" PORTAGE_DEBUG="0" PORTAGE_DEPCACHEDIR="/var/cache/edb/dep" PORTAGE_ELOG_CLASSES="log warn error" PORTAGE_ELOG_MAILFROM="portage@localhost" PORTAGE_ELOG_MAILSUBJECT="[portage] ebuild log for ${PACKAGE} on ${HOST}" PORTAGE_ELOG_MAILURI="root" PORTAGE_ELOG_SYSTEM="save_summary:log,warn,error,qa echo" PORTAGE_FETCH_CHECKSUM_TRY_MIRRORS="5" PORTAGE_FETCH_RESUME_MIN_SIZE="350K" PORTAGE_GID="250" PORTAGE_GPG_SIGNING_COMMAND="gpg --sign --digest-algo SHA256 --clearsign --yes --default-key "${PORTAGE_GPG_KEY}" --homedir "${PORTAGE_GPG_DIR}" "${FILE}"" PORTAGE_INST_GID="0" PORTAGE_INST_UID="0" PORTAGE_INTERNAL_CALLER="1" PORTAGE_OVERRIDE_EPREFIX="" PORTAGE_PYM_PATH="/usr/lib64/portage/pym" 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_RSYNC_RETRIES="-1" PORTAGE_SYNC_STALE="30" PORTAGE_TMPDIR="/var/tmp" PORTAGE_VERBOSE="1" PORTAGE_WORKDIR_MODE="0700" PORTAGE_XATTR_EXCLUDE="security.*" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/haskell /var/lib/layman/sage-on-gentoo /var/lib/layman/progress" PORT_LOGDIR_CLEAN="find "${PORT_LOGDIR}" -type f ! -name "summary.log*" -mtime +7 -delete" PRELINK_PATH_MASK="/usr/lib64/libfreebl3.so:/usr/lib64/libnssdbm3.so:/usr/lib64/libsoftokn3.so" PROFILE_ONLY_VARIABLES="ARCH ELIBC IUSE_IMPLICIT KERNEL USERLAND USE_EXPAND_IMPLICIT USE_EXPAND_UNPREFIXED USE_EXPAND_VALUES_ARCH USE_EXPAND_VALUES_ELIBC USE_EXPAND_VALUES_KERNEL USE_EXPAND_VALUES_USERLAND" PWD="/root" PYTHONDONTWRITEBYTECODE="1" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="x86_64 i386" QEMU_USER_TARGETS="x86_64 i386" QT_GRAPHICSSYSTEM="raster" QT_PLUGIN_PATH="/usr/lib64/kde4/plugins" RESUMECOMMAND="wget -c -t 3 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}"" RESUMECOMMAND_RSYNC="rsync -avP "${URI}" "${DISTDIR}/${FILE}"" RESUMECOMMAND_SSH="bash -c "x=\${2#ssh://} ; host=\${x%%/*} ; port=\${host##*:} ; host=\${host%:*} ; [[ \${host} = \${port} ]] && port=22 ; exec rsync --rsh=\"ssh -p\${port}\" -avP \"\${host}:/\${x#*/}\" \"\$1\"" rsync "${DISTDIR}/${FILE}" "${URI}"" ROOT="/" ROOTPATH="/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.6.3" RPMDIR="/usr/portage/rpm" RUBYOPT="-rauto_gem" RUBY_TARGETS="ruby19" R_HOME="/usr/lib64/R" SHELL="/bin/zsh" SHLVL="1" SYMLINK_LIB="yes" SYNC="rsync://rsync.gentoo.org/gentoo-portage" TERM="rxvt-unicode" UNINSTALL_IGNORE="/lib/modules/*" USE="X aac acl alsa amd64 berkdb bluetooth bzip2 cdda cdrom cli consolekit cracklib crypt cxx dbus djvu dri dvd ffmpeg fftw flac fortran gdbm gif gpm iconv imagemagick inotify ipv6 jpeg kde kdepim lapack libsamplerate lzma mmx modules mp3 mpeg mpi mudflap multilib ncurses nls nptl ogg opengl openmp openssl openvg pam pcre png policykit pulseaudio qt3support qt4 readline romio samba semantic-desktop session spice sse sse2 ssl ssse3 svg tcpd theora threads tiff truetype udisks unicode v4l vaapi vorbis vpx x264 xft xinerama zlib zsh-completion" ABI_X86="64" 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="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" DRACUT_MODULES="crypt" 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 synaptics keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="fr en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="x86_64 i386" QEMU_USER_TARGETS="x86_64 i386" RUBY_TARGETS="ruby19" USERLAND="GNU" VIDEO_CARDS="intel" 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" USER="root" USERLAND="GNU" USE_EXPAND="ABI_X86 ALSA_CARDS ALSA_PCM_PLUGINS APACHE2_MODULES APACHE2_MPMS CALLIGRA_FEATURES CAMERAS COLLECTD_PLUGINS CROSSCOMPILE_OPTS CURL_SSL DRACUT_MODULES DVB_CARDS ELIBC ENLIGHTENMENT_MODULES FCDSL_CARDS FFTOOLS FOO2ZJS_DEVICES FRITZCAPI_CARDS GPSD_PROTOCOLS GRUB_PLATFORMS INPUT_DEVICES KERNEL LCD_DEVICES LIBREOFFICE_EXTENSIONS LINGUAS LIRC_DEVICES MISDN_CARDS NETBEANS_MODULES NGINX_MODULES_HTTP NGINX_MODULES_MAIL OFED_DRIVERS OFFICE_IMPLEMENTATION OPENMPI_FABRICS OPENMPI_OFED_FEATURES OPENMPI_RM PHP_TARGETS PYTHON_SINGLE_TARGET PYTHON_TARGETS QEMU_SOFTMMU_TARGETS QEMU_USER_TARGETS RUBY_TARGETS SANE_BACKENDS USERLAND VIDEO_CARDS VOICEMAIL_STORAGE XFCE_PLUGINS XTABLES_ADDONS" USE_EXPAND_HIDDEN="CROSSCOMPILE_OPTS ELIBC KERNEL USERLAND" USE_EXPAND_IMPLICIT="ARCH ELIBC KERNEL USERLAND" USE_EXPAND_UNPREFIXED="ARCH" USE_EXPAND_VALUES_ARCH="alpha amd64 amd64-fbsd amd64-linux arm arm-linux hppa hppa-hpux ia64 ia64-hpux ia64-linux m68k m68k-mint mips ppc ppc64 ppc64-linux ppc-aix ppc-macos ppc-openbsd s390 sh sparc sparc64-freebsd sparc64-solaris sparc-fbsd sparc-solaris x64-freebsd x64-macos x64-openbsd x64-solaris x86 x86-cygwin x86-fbsd x86-freebsd x86-interix x86-linux x86-macos x86-netbsd x86-openbsd x86-solaris x86-winnt" USE_EXPAND_VALUES_ELIBC="AIX Cygwin Darwin FreeBSD glibc HPUX Interix mintlib NetBSD OpenBSD SunOS uclibc Winnt" USE_EXPAND_VALUES_KERNEL="AIX Cygwin Darwin FreeBSD freemint HPUX Interix linux NetBSD OpenBSD SunOS Winnt" USE_EXPAND_VALUES_USERLAND="BSD GNU" USE_ORDER="env:pkg:conf:defaults:pkginternal:repo:env.d" VIDEO_CARDS="intel" VTKHOME="/usr" VTK_DATA_ROOT="/usr/share/vtk/data" VTK_DIR="/usr/lib64/vtk-5.10" XAUTHORITY="/root/.xauthEa9OlU" XDG_CONFIG_DIRS="/etc/xdg" XDG_DATA_DIRS="/usr/local/share:/usr/share" 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" _="/usr/bin/emerge"
Created attachment 347474 [details] build.log
I fixed the blas/lapck issue, but it seems to incompatible to in tree umfpack.
+ 06 May 2013; Justin Lecher <jlec@gentoo.org> pysparse-1.1.1-r1.ebuild: + USe internal umfpack due to incompatibility with latest umfpack from tree +
