Bug 398195 – [science overlay] mgltools-pyglf-1.5.6_rc2 fails to emerge due to missing libreflapack.so

• Product: Gentoo Linux
• Status: RESOLVED INVALID

[Description Juergen Rose 2012-01-08 22:33:54 UTC]

'emerge mgltools-pyglf' fails with:
...
>>> Emerging (1 of 11) sci-chemistry/mgltools-pyglf-1.5.6_rc2 from science
 * mgltools_source_1.5.6rc2.tar.gz RMD160 SHA1 SHA256 size ;-) ...                                                                                                             [ ok ]
>>> Unpacking source...
>>> Source unpacked in /var/tmp/portage/sci-chemistry/mgltools-pyglf-1.5.6_rc2/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/mgltools-pyglf-1.5.6_rc2/work/pyglf-1.5.6 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/mgltools-pyglf-1.5.6_rc2/work/pyglf-1.5.6 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/mgltools-pyglf-1.5.6_rc2/work/pyglf-1.5.6 ...
 * Building of sci-chemistry/mgltools-pyglf-1.5.6_rc2 with CPython 2.7...
python2.7 setup.py build -b build-2.7
Traceback (most recent call last):
  File "setup.py", line 18, in <module>
    import numpy
  File "/usr/lib64/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
  File "/usr/lib64/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib64/python2.7/site-packages/numpy/lib/__init__.py", line 13, in <module>
    from polynomial import *
  File "/usr/lib64/python2.7/site-packages/numpy/lib/polynomial.py", line 17, in <module>
    from numpy.linalg import eigvals, lstsq
  File "/usr/lib64/python2.7/site-packages/numpy/linalg/__init__.py", line 48, in <module>
    from linalg import *
  File "/usr/lib64/python2.7/site-packages/numpy/linalg/linalg.py", line 23, in <module>
    from numpy.linalg import lapack_lite
ImportError: libreflapack.so: cannot open shared object file: No such file or directory
 * ERROR: sci-chemistry/mgltools-pyglf-1.5.6_rc2 failed (compile phase):




root@wildcat:/root(43)# emerge --info =sci-chemistry/mgltools-pyglf-1.5.6_rc2
Portage 2.1.10.44 (default/linux/amd64/10.0/desktop, gcc-4.5.3, glibc-2.14.1-r2, 3.1.6-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.1.6-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T7300_@_2.00GHz-with-gentoo-2.1
Timestamp of tree: Sun, 08 Jan 2012 21:30:01 +0000
app-shells/bash:          4.2_p20
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r3, 3.2.2
dev-util/cmake:           2.8.6-r4
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1
sys-apps/openrc:          0.9.8
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.2
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.5.3-r2
sys-devel/gcc-config:     1.5-r2
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r3
sys-kernel/linux-headers: 3.2 (virtual/os-headers)
sys-libs/glibc:           2.14.1-r2
Repositories: gentoo sunrise lordvan science x-portage x-cpan x-g-octave
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft Oracle-BCLA-JavaSE"
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/env.d/java/ /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=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j1"
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/sunrise /var/lib/layman/lordvan /var/lib/layman/science /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="64bit R X Xaw3d a52 aac acl acpi afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit cracklib crypt css cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack laptop latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lua lzo mad mail maildir mapnik math matroska mkl mmx mng modules mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nptl nptlonly nsplugin ntp numpy obex objc ocaml ocr octave odbc ogdi ogg ole openexr opengl openmp overview pam pango pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 ssl ssse3 startup-notification subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thinkpad threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales vaapi video virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" 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" DVB_CARDS="usb-wt220u" 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="de fr" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" 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"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS


root@wildcat:/root(44)# emerge -pqv =sci-chemistry/mgltools-pyglf-1.5.6_rc2
[ebuild  N    ] sci-chemistry/mgltools-pyglf-1.5.6_rc2

[Comment 1 Juergen Rose 2012-01-08 22:50:10 UTC]

After reemerging numpy the issue disapeared.

[Comment 2 Justin Lecher (RETIRED) 2012-01-09 08:12:20 UTC]

So it is fixed?

[Comment 3 Juergen Rose 2012-01-09 10:24:56 UTC]

It seems that it is fixed.