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Bug 375447 - sci-chemistry/coot-0.6.2 with USE=openmp fails to link
Summary: sci-chemistry/coot-0.6.2 with USE=openmp fails to link
Status: RESOLVED DUPLICATE of bug 349078
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Gentoo Chemistry-Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2011-07-17 10:21 UTC by David Kredba
Modified: 2011-07-17 10:39 UTC (History)
0 users

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


Attachments
coot buildlog use=openmp (build.log.gz,27.46 KB, application/octet-stream)
2011-07-17 10:22 UTC, David Kredba
Details

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Description David Kredba 2011-07-17 10:21:08 UTC
Sci-chemistry/coot-0.6.2 with USE=openmp fails to link:

...
-lrt -pthread
/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_parallel_start'
/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_critical_name_end'
/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_loop_dynamic_start'
/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_critical_name_start'
/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_loop_end_nowait'
/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_loop_dynamic_next'
/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_parallel_end'
collect2: ld returned 1 exit status

Please see attched build log.

Reproducible: Always

Steps to Reproduce:
1. Be ~amd64, gcc-4.6.1
2. Upgrade coot from 0.6.1 to 0.6.2
3. 
Actual Results:  
Link time error for coot-real.

Expected Results:  
Links fine.

With USE=-openmp links fine and ran fine.

emerge --info
Portage 2.2.0_alpha45 (default/linux/amd64/10.0/desktop/kde, gcc-4.6.1, glibc-2.13-r4, 2.6.39-gentoo-r3-2d x86_64)
=================================================================
System uname: Linux-2.6.39-gentoo-r3-2d-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9550_@_2.83GHz-with-gentoo-2.0.3
Timestamp of tree: Sun, 17 Jul 2011 05:30:01 +0000
app-shells/bash:          4.2_p10
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2, 3.2
dev-util/cmake:           2.8.5
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.8.3-r1
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-r1
sys-devel/binutils:       2.21.1
sys-devel/gcc:            4.6.1
sys-devel/gcc-config:     1.5-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 2.6.38 (virtual/os-headers)
sys-libs/glibc:           2.13-r4
Repositories: gentoo
Installed sets: 
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -ggdb -march=core2"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /var/bind /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /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="-O2 -pipe -ggdb -march=core2"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe -ggdb -march=core2"
GENTOO_MIRRORS="ftp://gentoo.mirror.web4u.cz/"
LANG="cs_CZ.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="cs en"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_COMPRESS="echo"
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=""
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo caps cdda cdr cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gdu gif gmp gpm gtk iconv idn ithreads java jpeg jpeg2k kde kipi lcms ldap libnotify lzma mad mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl nptlonly objc objc++ objc-gc odbc ogg openexr opengl openmp pam pango pcre pdf perl phonon plasma png policykit ppds pppd python qt3support qt4 readline samba sdl semantic-desktop session slang speex spell sqlite sse sse2 ssl ssse3 svg sysfs tcl tcpd threads tiff tk truetype udev unicode usb vorbis wavpack x264 xattr xcb xcomposite xinerama xml xorg xscreensaver xulrunner xv xvid xvmc zlib" 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="braindump flow karbon kexi kpresenter krita tables words" 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="evdev keyboard mouse joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="cs en" LIRC_DEVICES="inputlirc pctv hauppauge hauppauge_dvb devinput" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nouveau" 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_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 David Kredba 2011-07-17 10:22:06 UTC
Created attachment 280215 [details]
coot buildlog use=openmp
Comment 2 Agostino Sarubbo gentoo-dev 2011-07-17 10:38:06 UTC
is know that is broken, I test it with jlec time ago.
Comment 3 Justin Lecher (RETIRED) gentoo-dev 2011-07-17 10:39:21 UTC

*** This bug has been marked as a duplicate of bug 349078 ***