Bug 473680 – [science-overlay] sci-chemistry/modeller-9.12 link /opt/modeller/lib/x86_64-intel8/libmodeller.so points to /opt/modeller/lib/x86_64-intel8/libmodeller.so.5 which does not exist

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Juergen Rose 2013-06-18 09:30:33 UTC]

'emerge modeller' complaines about:
...
>>> /opt/modeller/lib/
>>> /opt/modeller/lib/x86_64-intel8/
>>> /opt/modeller/lib/x86_64-intel8/libsaxs.so
>>> /opt/modeller/lib/x86_64-intel8/libhdf5_hl.so.7
>>> /opt/modeller/lib/x86_64-intel8/libifcore.so.5
>>> /opt/modeller/lib/x86_64-intel8/libpython2.3.so.1.0
>>> /opt/modeller/lib/x86_64-intel8/libsvml.so
>>> /opt/modeller/lib/x86_64-intel8/libmodeller.so.8
...
 * QA Notice: Symbolic link /opt/modeller/lib/x86_64-intel8/libmodeller.so points to /opt/modeller/lib/x86_64-intel8/libmodeller.so.5 which does not exist.
>>> /opt/modeller/lib/x86_64-intel8/libmodeller.so -> libmodeller.so.5


'revdep-rebuild' complaines too.


root@impala:/usr/src(42)# emerge --info modeller
Portage 2.1.12.5 (default/linux/amd64/13.0, gcc-4.7.3, glibc-2.17, 3.9.6-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.9.6-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.2
KiB Mem:     8165512 total,    994812 free
KiB Swap:   50347696 total,  50300224 free
Timestamp of tree: Tue, 18 Jun 2013 07:00:01 +0000
ld GNU ld (GNU Binutils) 2.23.1
app-shells/bash:          4.2_p45
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.5, 3.2.5, 3.3.2
dev-util/cmake:           2.8.11.1
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.13.4
sys-devel/binutils:       2.23.1
sys-devel/gcc:            4.6.4, 4.7.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.9 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo x11 science sage-on-gentoo sunrise sabayon x-portage x-cpan g-octave
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=amdfam10 -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/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.5/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=amdfam10 -O2 -pipe"
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 strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.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="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/science /var/lib/layman/sage-on-gentoo /var/lib/layman/sunrise /var/lib/layman/sabayon /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac accessibility acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boo boost bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli cmake consolekit corba cracklib crypt css cuda cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fts3 fuse g3dvl gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glib glpk gml gmp gnome gnome-keyring gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile harness hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3 id3tag ide imagemagick imap inotify introspection ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kqemu kvm ladspa lame lapack latex lcms ldap lensfun libffi libkms libnotify libsamplerate live lm_sensors lua lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nsplugin ntfs ntp numpy nvidia obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp overview pam pcre pda pdf perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline real reiserfs reports rhythmbox rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 sse4a ssl stlport subtitles subversion sudo suexec svg svm swig szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus threads thunderbird tidy tiff tk tools truetype udev udisks unicode usb userlocales utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" 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" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DRACUT_MODULES="caps lvm mdraid 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 void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" 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

=================================================================
                        Package Settings
=================================================================

sci-chemistry/modeller-9.12 was built with the following:
USE="doc examples" PYTHON_TARGETS="python2_7 -python2_6"

[Comment 1 Justin Lecher (RETIRED) 2013-06-18 12:46:43 UTC]

+*modeller-9.12-r1 (18 Jun 2013)
+
+  18 Jun 2013; Justin Lecher <[e-mail]> -modeller-9.12.ebuild,
+  +modeller-9.12-r1.ebuild:
+  Fix broken symlink, #473680
+

[Comment 2 Juergen Rose 2013-06-19 13:42:18 UTC]

There is still something wrong with sci-chemistry/modeller, every 'revdep-rebuild' is rebuilding modeller:

root@impala:/root(26)# genlop -t modeller | tail -n 15
     Tue Jun 18 10:32:06 2013 >>> sci-chemistry/modeller-9.12
       merge time: 52 seconds.

     Tue Jun 18 11:22:48 2013 >>> sci-chemistry/modeller-9.12
       merge time: 45 seconds.

     Wed Jun 19 10:41:44 2013 >>> sci-chemistry/modeller-9.12-r1
       merge time: 54 seconds.

     Wed Jun 19 11:50:35 2013 >>> sci-chemistry/modeller-9.12-r1
       merge time: 56 seconds.

     Wed Jun 19 12:27:34 2013 >>> sci-chemistry/modeller-9.12-r1
       merge time: 54 seconds.


root@impala:/root(27)# revdep-rebuild
 * Configuring search environment for revdep-rebuild

 * Checking reverse dependencies
 * Packages containing binaries and libraries broken by a package update
 * will be emerged.

 * Collecting system binaries and libraries
 * Generated new 1_files.rr
 * Collecting complete LD_LIBRARY_PATH
 * Generated new 2_ldpath.rr
 * Checking dynamic linking consistency
[ 87% ]  *   broken /usr/lib64/python2.7/site-packages/_modeller.so (requires libmodeller.so.8)
[ 100% ]                 
 * Generated new 3_broken.rr
 * Assigning files to packages
 * Generated new 4_ebuilds.rr
 * Evaluating package order
 * Generated new 5_order.rr
 * All prepared. Starting rebuild
emerge --complete-graph=y --oneshot   sci-chemistry/modeller:0
..........
Calculating dependencies... done!

>>> Verifying ebuild manifests

>>> Emerging (1 of 1) sci-chemistry/modeller-9.12-r1 from science
 * modeller-9.12.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ..              [ ok ]
>>> Unpacking source...
...
root@impala:/root(28)# qfile -v /usr/lib64/python2.7/site-packages/_modeller.so
sci-chemistry/modeller-9.12-r1 (/usr/lib64/python2.7/site-packages/_modeller.so)
root@impala:/root(29)# ll /usr/lib64/python2.7/site-packages/_modeller.so
-rwxr-xr-x 1 root root 601112 Jun 19 15:33 /usr/lib64/python2.7/site-packages/_modeller.so*
root@impala:/root(30)# ldd /usr/lib64/python2.7/site-packages/_modeller.so
        linux-vdso.so.1 (0x00007fffe97ff000)
        libmodeller.so.8 => not found
        libglib-2.0.so.0 => /usr/lib64/libglib-2.0.so.0 (0x00007f58d866a000)
        libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x00007f58d82a2000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f58d8085000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f58d7cd3000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f58d7acb000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f58d78c7000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00007f58d76c3000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f58d73c5000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f58d8cae000)


/opt/modeller/lib/x86_64-intel8/libmodeller.so.8 is not found:

root@impala:/root(32)# ll /opt/modeller/lib/x86_64-intel8/libmodeller.so.8
-rwxr-xr-x 1 root root 3429856 Jun 19 15:33 /opt/modeller/lib/x86_64-intel8/libmodeller.so.8*
root@impala:/root(33)# qfile -v /opt/modeller/lib/x86_64-intel8/libmodeller.so.8
sci-chemistry/modeller-9.12-r1 (/opt/modeller/lib/x86_64-intel8/libmodeller.so.8)

[Comment 3 Juergen Rose 2013-06-25 07:56:16 UTC]

Should I file a separate bug for the last issue (comment 2)?

[Comment 4 Justin Lecher (RETIRED) 2013-06-25 08:00:38 UTC]

(In reply to Juergen Rose from comment #3)
> Should I file a separate bug for the last issue (comment 2)?

Please do. I know what the issue is, but I didn't have to time to fix it.

Temporarily you can create a symlink like sthis

ln -sf /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 /usr/lib/libmodeller.so.8