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Bug 295976 - sci-misc/salome-meta-3.2.6 from science overlay fails to install because of qwt version conflict
Summary: sci-misc/salome-meta-3.2.6 from science overlay fails to install because of q...
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Gentoo Science Related Packages
Depends on:
Reported: 2009-12-06 15:41 UTC by Juergen Rose
Modified: 2010-03-15 15:58 UTC (History)
1 user (show)

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


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Description Juergen Rose 2009-12-06 15:41:47 UTC
'emerge salome-meta' wants to install qwt-4.2.0-r3 which conflicts with installed qwt-5.2.0. If fails with:
>>> Installing (4 of 18) x11-libs/qwt-4.2.0-r3
 * checking 614 files for package collisions
 * This package will overwrite one or more files that may belong to other
 * packages (see list below). You can use a command such as `portageq
 * Detected file collision(s):
 *      /usr/share/man/man3/QwtDialScaleDraw.3.bz2
 *      /usr/share/man/man3/QwtText.3.bz2
 * Searching all installed packages for file collisions...
 * Press Ctrl-C to Stop
 * x11-libs/qwt-5.2.0
 *      /usr/share/man/man3/QwtAnalogClock.3.bz2
 * Package 'x11-libs/qwt-4.2.0-r3' NOT merged due to file collisions. If
 * necessary, refer to your elog messages for the whole content of the
 * above message.

>>> Failed to install x11-libs/qwt-4.2.0-r3, Log file:

Reproducible: Always

root@lynx:/root(8)# emerge --info
Portage (default/linux/amd64/10.0/desktop, gcc-4.4.2, glibc-2.11-r1, 2.6.32 x86_64)
System uname: Linux-2.6.32-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.0.1
Timestamp of tree: Sun, 06 Dec 2009 08:30:24 +0000
app-shells/bash:     4.0_p35
dev-java/java-config: 2.1.10
dev-lang/python:     2.6.4, 3.1.1-r1
dev-python/pycrypto: 2.1.0_beta1
dev-util/cmake:      2.8.0
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.5.3
sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.13, 2.64
sys-devel/automake:  1.4_p6, 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11
sys-devel/binutils:  2.20
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.30-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config /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/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/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=nocona -O2 -pipe -fomit-frame-pointer"
FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch"
FFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer"
LINGUAS="de fr"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTDIR_OVERLAY="/usr/local/portage/layman/n4g /usr/local/portage/layman/dotnet /usr/local/portage/layman/science /usr/local/portage/layman/java-overlay /usr/local/portage/layman/suka /usr/local/portage/layman/zugaina /usr/local/portage/layman/x11 /usr/local/portage"
USE="X Xaw3d a52 aac acl acpi administrator afs aiglx alsa amd64 amrr ao aotuv apache2 asf aspell atlas auctex audacious audiofile automount bash-completion beagle berkdb bjam blas bluetooth bonobo boo boost branding bzip2 c++ cairo cardbus cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib cran crypt cups curl cxx daap dbus device-mapper dga dia divx djvu dlloader dmi dns doc dri ds3490 dts dv dvb dvd dvdr dvi dxr3 dynagraph eds effects elf emacs emboss encode epiphany esd evo examples exif expat extra extras fam fame ffmpeg fftw firefox fits flac fltk foomaticdb fortran fpx fuse galago garmin gd gdal gdbm geolocation geos gif gimp gimpprint ginac git glade glib glitz gml gmp gnokii gnome gnome-keyring gnuplot gnutls gphoto2 gpm graphics graphviz gs gsl gsm gstreamer gtk guile hal hardened harness hddtemp hdf hdf5 hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb ipod ipv6 irda irmc ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kde kde4 kerberos kexi keyring kpathsea kvm ladspa lame lapack laptop latex lcms ldap libffi libgda libnotify libsamplerate lirc lua lzo lzw mad maildir mailwrapper math matroska mikmod mmx mmxext mng mod modules mono motif mozdevelop mozilla mozsvg mozxmlterm mp3 mp4 mp4live mpeg mpeg2 mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp pae pam pcre pda pdf perl pipechan plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python qhull qt3support qt4 quicktime readline reflection reiserfs rhythmbox rle rpc rrdcgi rrdtool samba sasl science sdl server session slang slp smbclient smp sndfile snmp soup sox speex spell spl sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg sysfs szip t1lib tcl tcpd tex theora thinkpad threads thunar thunderbird tidy tiff tk tntc truetype unicode usb userlocales utempter v4l2 vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" 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 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="canon" DVB_CARDS="usb-wt220u" ELIBC="glibc" 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="ide websvccommon nb harness apisupport groovy gsf j2ee java xml" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa" 
Comment 1 Juergen Rose 2010-03-03 19:31:30 UTC
It now fails with:

root@moose:/root(27)# emerge -pvD salome-meta

These are the packages that would be merged, in order:

Calculating dependencies... done!

emerge: there are no ebuilds to satisfy "x11-libs/qwt:0".
(dependency required by "sci-misc/salome-kernel-3.2.6" [ebuild])
(dependency required by "sci-misc/salome-pycalculator-3.2.6" [ebuild])
(dependency required by "sci-misc/salome-meta-3.2.6" [ebuild])
(dependency required by "salome-meta" [argument])
Comment 2 Etienne Lorriaux 2010-03-14 23:50:43 UTC
Hi Juergen,

in fact salome-3.2.6 was totally obsolete, relying on obsolete dependencies. It was impossible to maintain this version. We were having the same kind of problems trying to package newer versions, I've just removed salome-*-3.2.6 ebuilds from the overlay and pushed new 5.1.3 versions 


Could you please close this bug please?

Thanks, Etienne.
Comment 3 Juergen Rose 2010-03-15 13:52:46 UTC
'emerge -vuDN salome-meta' fails now with:
/bin/sh ../../libtool --tag=CXX   --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../include  -I../../include -I/usr/include  -march=nocona -O2 -pipe -fomit-frame-pointer -DH5_USE_16_API -MT MEDversionedApiF.lo -MD -MP -MF .deps/MEDversionedApiF.Tpo -c -o MEDversionedApiF.lo MEDversionedApiF.cxx
libtool: compile:  x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../include -I../../include -I/usr/include -march=nocona -O2 -pipe -fomit-frame-pointer -DH5_USE_16_API -MT MEDversionedApiF.lo -MD -MP -MF .deps/MEDversionedApiF.Tpo -c MEDversionedApiF.cxx  -fPIC -DPIC -o .libs/MEDversionedApiF.o
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/include/g++-v4/utility:62,
                 from /usr/include/openmpi/ompi/mpi/cxx/mpicxx.h:37,
                 from /usr/include/mpi.h:1886,
                 from /usr/include/H5public.h:57,
                 from /usr/include/hdf5.h:24,
                 from ../../include/med.h:22,
                 from ../../include/med_misc.h:22,
                 from ../../include/MEDversionedApi.hxx:10,
                 from MEDversionedApiF.cxx:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/include/g++-v4/bits/stl_relops.h:83: error: template with C linkage
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/include/g++-v4/bits/ios_base.h: In function 'std::_Ios_Openmode std::operator&(std::_Ios_Openmode, std::_Ios_Openmode)':
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/include/g++-v4/bits/ios_base.h:124: error: declaration of C function 'std::_Ios_Openmode std::operator&(std::_Ios_Openmode, std::_Ios_Openmode)' conflicts with
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/include/g++-v4/bits/ios_base.h:84: error: previous declaration 'std::_Ios_Fmtflags std::operator&(std::_Ios_Fmtflags, std::_Ios_Fmtflags)' here
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/include/g++-v4/bits/ios_base.h: In function 'std::_Ios_Openmode std::operator|(std::_Ios_Openmode, std::_Ios_Openmode)':
/usr/include/openmpi/ompi/mpi/cxx/functions_inln.h:147: error: 'int MPI::Init_thread(int&, char**&, int)' should have been declared inside 'MPI'
/usr/include/openmpi/ompi/mpi/cxx/functions_inln.h: In function 'int MPI::Init_thread(int&, char**&, int)':
/usr/include/openmpi/ompi/mpi/cxx/functions_inln.h:147: error: declaration of C function 'int MPI::Init_thread(int&, char**&, int)' conflicts with
/usr/include/openmpi/ompi/mpi/cxx/functions_inln.h:137: error: previous declaration 'int MPI::Init_thread(int)' here
make[2]: *** [MEDversionedApiF.lo] Error 1
 * ERROR: sci-libs/med-2.3.5 failed:

I have openmpi installed:
root@lynx:/root(17)# qlist -Iv mpi

Comment 4 Justin Lecher (RETIRED) gentoo-dev 2010-03-15 15:56:54 UTC
Closed on request @irc by etienne.
Comment 5 Justin Lecher (RETIRED) gentoo-dev 2010-03-15 15:57:07 UTC
reopen to close correctly
Comment 6 Justin Lecher (RETIRED) gentoo-dev 2010-03-15 15:58:38 UTC
The ebuild in question is gone.