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Bug 361411 - sci-biology/transfac-3.2 fails to install because of Segmentation fault during indexing
Summary: sci-biology/transfac-3.2 fails to install because of Segmentation fault durin...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
: 401943 (view as bug list)
Depends on:
Blocks:
 
Reported: 2011-03-31 06:32 UTC by Juergen Rose
Modified: 2016-05-05 08:43 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


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Description Juergen Rose 2011-03-31 06:32:14 UTC
'emerge transfac' fails with:
>>> Emerging (1 of 21) sci-biology/transfac-3.2
 * transfac32.tar.Z RMD160 SHA1 SHA256 size ;-) ...                                                                         [ ok ]
 * Package:    sci-biology/transfac-3.2
 * Repository: gentoo
 * Maintainer: sci-biology@gentoo.org
 * USE:        amd64 elibc_glibc emboss kernel_linux multilib userland_GNU
 * FEATURES:   sandbox
>>> Unpacking source...
>>> Unpacking transfac32.tar.Z to /var/tmp/portage/sci-biology/transfac-3.2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/transfac-3.2/work
>>> Compiling source in /var/tmp/portage/sci-biology/transfac-3.2/work ...

 * Indexing TRANSFAC for usage with EMBOSS.
/var/tmp/portage/sci-biology/transfac-3.2/temp/environment: line 233: 13755 Segmentation fault      EMBOSS_DATA=. tfextract -auto -infile class.dat
 * ERROR: sci-biology/transfac-3.2 failed (compile phase):
 *   Indexing TRANSFAC failed.
 * 


Reproducible: Always




root@impala:/root(9)# emerge --info =sci-biology/transfac-3.2
Portage 2.1.9.45 (default/linux/amd64/10.0, gcc-4.5.2, glibc-2.13-r2, 2.6.38-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-2.6.38-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.0.2
Timestamp of tree: Wed, 30 Mar 2011 06:00:01 +0000
app-shells/bash:     4.2_p8
dev-java/java-config: 2.1.11-r3
dev-lang/python:     2.7.1-r1, 3.1.3-r1
dev-util/cmake:      2.8.4
sys-apps/baselayout: 2.0.2
sys-apps/openrc:     0.8.0
sys-apps/sandbox:    2.5
sys-devel/autoconf:  2.13, 2.68
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.21
sys-devel/gcc:       4.5.2
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.4-r1
sys-devel/make:      3.82
virtual/os-headers:  2.6.38 (sys-kernel/linux-headers)
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft"
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/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/ext-active/ /etc/php/cli-php5.3/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"
FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j5"
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/science /var/lib/layman/x11 /var/lib/layman/sunrise /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 abiword accessibility acl acpi admin afs alsa amd64 amrr ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf empathy encode epiphany evo examples exif expat extensions extra extras fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile harness hddtemp hdf hdf5 hdri http httpd hvm iconv icq icu id3 imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mailwrapper mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pam pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript pppd preview-latex proj projectx pstricks pulseaudio pymol python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl 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 sse4a ssl subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 video virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets xattr xcb xemacs xext 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 auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file 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 log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" 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 synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" 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="nv nouveau 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, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS


root@impala:/root(10)# emerge -pqv =sci-biology/transfac-3.2
[ebuild  N    ] sci-biology/transfac-3.2  USE="emboss -minimal"
Comment 1 Juergen Rose 2011-03-31 06:33:03 UTC
In /var/tmp/portage/sci-biology/transfac-3.2/temp/build.log is not more information than in the last posting
Comment 2 Juergen Rose 2011-03-31 11:10:16 UTC
At line 233 in /var/tmp/portage/sci-biology/transfac-3.2/temp/environment is the function src_install defined as:

src_install () 
{ 
    if ! use minimal; then
        insinto /usr/share/${PN}-${SLOT};
        doins *.dat || die;
    fi;
    if use emboss; then
        insinto /usr/share/EMBOSS/data;
        doins tf* || die;
    fi
}
Comment 3 Juergen Rose 2011-03-31 11:20:25 UTC
Sorry the last comment was not correct at line 233 is the function src_compile, which is defined as:

src_compile () 
{ 
    if use emboss; then
        echo;
        einfo "Indexing TRANSFAC for usage with EMBOSS.";
        EMBOSS_DATA=. tfextract -auto -infile class.dat || die "Indexing TRANSFAC failed.";
        echo;
    fi
}

tfextract belongs to emboss-6.3.1_p4-r1. Reinstalling sci-biology/emboss did not improve the issue.
Comment 4 Juergen Rose 2011-03-31 11:48:41 UTC
After downgrading to sci-biology/emboss-6.1.0-r1 I could emerge transfac.
Comment 5 Juergen Rose 2011-04-01 07:36:13 UTC
But after downgrading to sci-biology/emboss-6.1.0-r1 sci-biology/embassy-vienna-1.7.2-r2 does not emerge, because it depends on sci-biology/emboss-6.3.1_p4-r1.
Comment 6 Justin Lecher (RETIRED) gentoo-dev 2011-04-01 07:54:38 UTC
emboss-6.3.1 still has some problems. Don't use this on production systems.
Comment 7 Martin Mokrejš 2012-02-02 17:42:53 UTC
Ah, I hit the same bug and unfortunately opened bug #401943. But a stacktrace is attached to it. ;-) Before that patch the ebuild to drop the hardcoded "-O2" from configure.in: see bug #393311.
Comment 8 Toralf Förster gentoo-dev 2015-08-22 08:01:09 UTC
still fails here :

  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-kde-unstable_20150820-090512) at a hardened host acting as a tinderbox.

  Portage 2.2.20.1 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/kde, gcc-4.9.3, glibc-2.21-r1, 4.1.4-hardened x86_64)



Maybe adding tree-cleaner ?
Comment 9 Toralf Förster gentoo-dev 2016-05-05 08:43:34 UTC
*** Bug 401943 has been marked as a duplicate of this bug. ***