Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 591570 - sci-biology/vienna-rna-2.1.8 : x86_64-pc-linux-gnu-gcc: error: libgomp.spec: No such file or directory
Summary: sci-biology/vienna-rna-2.1.8 : x86_64-pc-linux-gnu-gcc: error: libgomp.spec: ...
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:
Depends on:
Blocks:
 
Reported: 2016-08-18 07:26 UTC by Toralf Förster
Modified: 2016-08-18 07:26 UTC (History)
0 users

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


Attachments
emerge-history.txt (emerge-history.txt,410.21 KB, text/plain)
2016-08-18 07:26 UTC, Toralf Förster
Details
environment (environment,188.87 KB, text/plain)
2016-08-18 07:26 UTC, Toralf Förster
Details
sci-biology:vienna-rna-2.1.8:20160818-050917.log (sci-biology:vienna-rna-2.1.8:20160818-050917.log,104.31 KB, text/plain)
2016-08-18 07:26 UTC, Toralf Förster
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2016-08-18 07:26:03 UTC
                          ^
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=native -O2 -pipe /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/temp.linux-x86_64-2.7/RNA_wrap.o -L../../lib -L/usr/lib64 -lRNA -lpython2.7 -o /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/lib/_RNA.so -fopenmp -lstdc++ -s
x86_64-pc-linux-gnu-gcc: error: libgomp.spec: No such file or directory


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

  This is an unstable amd64 chroot image (named amd64-desktop-unstable_20160811-160513) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------
  USE flags defined in ...

  ... make.conf:
USE="  pax_kernel xtpax -cdinstall -oci8 -bindist pax_kernel xtpax -cdinstall -oci8 -bindist aes-ni bugzilla cairo cdda cgoups custom-optimization dec_av2 designer dot evdev gles gnuplot gtkstyle gzip havege icu imap introspection jadetex lapack latex lzma mbox mod mpeg mssql multimedia multitarget mysql obj ogg pdo plasma rendering scripts sdl sourceview sqlite3 sslv2 system-libvpx usb xml captcha compressed-lumas dii extras gd -gif gnome -graphicsmagick graphtft gtk image-converter imagemagick input_testpicture jpeg latex ljr mapimg -minimal pdf png test videoslideshow wxwidgets fontconfig extra xetex qt5 sqlite pcre16 webkit printsupport widgets graph -qpm gpg -qt4 qt3support gnome-keyring minizip -dynamic -openmp python gles2 mod mikmod modplug xcb egl eglfs tk openexr plotutils !imlib utils ffmpeg fpm"

  ... /etc/portage/package.use/*:
  mail-mta/ssmtp    ssl mta
  net-misc/wget     ssl
  app-editors/emacs -dbus -svg -ssl -gtk -gtk3
  dev-util/cmake  -qt4 -qt5
  net-misc/iputils -caps -filecaps
  >=dev-libs/boehm-gc-7.4.2 threads
  app-text/poppler -qt5

  unmasked packages in /etc/portage/package.unmask/*:

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-4.9.3
 [2] x86_64-pc-linux-gnu-5.4.0 *
Available Java Virtual Machines:
  [1]   icedtea-bin-7 
  [2]   icedtea-bin-8  system-vm
Available Python interpreters, in order of preference:
  [1]   python3.4
  [2]   python2.7 (fallback)
  [3]   jython2.7 (fallback)
Available Ruby profiles:
  [1]   ruby20 (with Rubygems) *
  [2]   ruby21 (with Rubygems)
  -----------------------------------------------------------------

Portage 2.3.0 (python 3.4.5-final-0, default/linux/amd64/13.0/desktop, gcc-5.4.0, glibc-2.23-r2, 4.7.1-hardened x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.7.1-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16156084 total,   1911860 free
KiB Swap:   16777212 total,  16752028 free
Timestamp of repository gentoo: Thu, 18 Aug 2016 03:24:17 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1
ccache version 3.2.7 [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:          2.7.12::gentoo, 3.4.5::gentoo
dev-util/ccache:          3.2.7::gentoo
dev-util/cmake:           3.6.1::gentoo
sys-apps/baselayout:      2.2-r1::gentoo
sys-apps/openrc:          0.21.3::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:       2.26.1::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: 4.4::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/stunnel/stunnel.conf /opt/openfire/resources/security/ /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb /var/lib/i2pd/certificates"
CONFIG_PROTECT_MASK="/etc/angband/gamedata/ /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/php/cli-php7.0/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="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--verbose --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="!imlib X a52 aac acl acpi aes-ni alsa amd64 berkdb bluetooth branding bugzilla bzip2 cairo captcha cdda cdr cgoups cli compressed-lumas consolekit cracklib crypt cups custom-optimization cxx dbus dec_av2 designer dii dot dri dts dvd dvdr egl eglfs emboss encode evdev exif extra extras fam ffmpeg firefox flac fontconfig fortran fpm gd gdbm glamor gles gles2 gnome gnome-keyring gnuplot gpg gpm graph graphtft gtk gtkstyle gzip havege iconv icu image-converter imagemagick imap input_testpicture introspection ipv6 jadetex jpeg lapack latex lcms ldap libnotify ljr lzma mad mapimg mbox mikmod minizip mmx mmxext mng mod modplug modules mp3 mp4 mpeg mssql multilib multimedia multitarget mysql ncurses nls nptl obj ogg openexr opengl pam pango pax_kernel pcre pcre16 pdf pdo plasma plotutils png policykit ppds printsupport python qt3support qt5 readline rendering scripts sdl seccomp session sourceview spell sqlite sqlite3 sse sse2 ssl sslv2 startup-notification svg system-libvpx tcpd test tiff tk truetype udev udisks unicode upower usb utils videoslideshow vorbis webkit widgets wxwidgets x264 xattr xcb xetex xml xtpax xv xvid zlib" 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="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="keyboard mouse evdev" 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 2016-08-18 07:26:06 UTC
Created attachment 443654 [details]
emerge-history.txt
Comment 2 Toralf Förster gentoo-dev 2016-08-18 07:26:09 UTC
Created attachment 443656 [details]
environment
Comment 3 Toralf Förster gentoo-dev 2016-08-18 07:26:11 UTC
Created attachment 443658 [details]
sci-biology:vienna-rna-2.1.8:20160818-050917.log