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Bug 587470 - sci-biology/transfac-3.2 : * ERROR: sci-biology/transfac-3.2::gentoo failed (compile phase):
Summary: sci-biology/transfac-3.2 : * ERROR: sci-biology/transfac-3.2::gentoo failed ...
Status: RESOLVED DUPLICATE of bug 361411
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:
Depends on:
Blocks:
 
Reported: 2016-06-29 07:03 UTC by Toralf Förster
Modified: 2022-07-07 19:21 UTC (History)
0 users

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


Attachments
emerge-history.txt (emerge-history.txt,606.24 KB, text/plain)
2016-06-29 07:03 UTC, Toralf Förster
Details
environment (environment,14.23 KB, text/plain)
2016-06-29 07:03 UTC, Toralf Förster
Details
sci-biology:transfac-3.2:20160629-000532.log (sci-biology:transfac-3.2:20160629-000532.log,1.63 KB, text/plain)
2016-06-29 07:03 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2016-06-29 07:03:30 UTC
 * Indexing TRANSFAC for usage with EMBOSS.
/var/tmp/portage/sci-biology/transfac-3.2/temp/environment: line 251: 30897 Bus error               EMBOSS_DATA=. tfextract -auto -infile class.dat
 * ERROR: sci-biology/transfac-3.2::gentoo failed (compile phase):
 *   Indexing TRANSFAC failed.
 * 
 * Call stack:


$ cat emerge-info.txt
  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-gnome-unstable_20160615-225422) at a hardened host acting as a tinderbox.

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

  make.conf: USE="pax_kernel xtpax -cdinstall -oci8 -bindist aes-ni -avcodec bzip2 cairo -cgoups -compat csc dbus emacs extra -gnome-keyring graphtft gudev icu javascript kvm -libkms libvirtd llvm mpi ncurses -ogg png printsupport pwquality python qemu qt3support sqlite ssh-askpass ssl system-jpeg thinkpad ufed -uml vdpau X xinerama xinetd xmlreader xslt zip"

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

Portage 2.3.0 (python 3.4.4-final-0, default/linux/amd64/13.0/desktop/gnome, gcc-5.4.0, glibc-2.23-r2, 4.5.7-hardened-r4 x86_64)
=================================================================
System uname: Linux-4.5.7-hardened-r4-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16157888 total,   3246396 free
KiB Swap:   16777212 total,  16748792 free
Timestamp of repository gentoo: Tue, 28 Jun 2016 22:22:30 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
ccache version 3.2.5 [disabled]
app-shells/bash:          4.3_p46::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.11-r2::gentoo, 3.4.4::gentoo, 3.5.1-r3::gentoo
dev-util/ccache:          3.2.5::gentoo
dev-util/cmake:           3.5.2-r1::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.21::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.10.3-r2::gentoo, 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo, 5.4.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.6::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: 1

local
    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/entropy /etc/grs/systems.conf /etc/omega.conf /etc/stunnel/stunnel.conf /opt/openfire/resources/security/ /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/qpsmtpd/plugins /var/lib/hsqldb /var/rancid/.cloginrc /var/yp/Makefile"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/games/angband/gamedata/ /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="-march=native -O2 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--verbose-conflicts --color=n --nospinner --tree --quiet-build"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi aes-ni alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli colord consolekit cracklib crypt csc cups cxx dbus dri dts dvd dvdr eds emacs emboss encode evo exif extra fam firefox flac fortran gdbm gif glamor gnome gnome-online-accounts gpm graphtft gstreamer gtk gudev iconv icu introspection ipv6 javascript jpeg kvm lcms ldap libnotify libsecret libvirtd llvm mad mmx mmxext mng modules mp3 mp4 mpeg mpi multilib nautilus ncurses nls nptl opengl openmp pam pango pax_kernel pcre pdf png policykit ppds printsupport pulseaudio pwquality python qemu qt3support qt4 readline sdl seccomp session spell sqlite sse sse2 ssh-askpass ssl startup-notification svg system-jpeg tcpd thinkpad tiff tracker truetype udev udisks ufed unicode upower usb vdpau vorbis wxwidgets x264 xattr xcb xinerama xinetd xml xmlreader xslt xtpax xv xvid zip zlib" ABI_X86="64" ALSA_CARDS="hda-intel" 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" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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 ublox ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 1 Toralf Förster gentoo-dev 2016-06-29 07:03:33 UTC
Created attachment 439130 [details]
emerge-history.txt
Comment 2 Toralf Förster gentoo-dev 2016-06-29 07:03:36 UTC
Created attachment 439132 [details]
environment
Comment 3 Toralf Förster gentoo-dev 2016-06-29 07:03:38 UTC
Created attachment 439134 [details]
sci-biology:transfac-3.2:20160629-000532.log
Comment 4 David Seifert gentoo-dev 2022-07-07 19:21:14 UTC

*** This bug has been marked as a duplicate of bug 361411 ***