Bug 5386

Sorry, RPMs for Fedora 14 of course.

CC: (none) => schlecht
Target Milestone: --- => Mageia 1

I'll have a look at it.

CC: (none) => remi
Assignee: bugsquad => remi

Hi Grigory! I just imported UGENE into Cauldron. I don't know this software so I'd be pleased if you could test my package and make sure that it works as intended.

If you are on Mageia 3 or 4, you should be able to create your own backport following this detailed howto: https://wiki.mageia.org/en/How_to_do_your_own_backports

You could also try to install the Cauldron RPM directly (on Mageia 4, I don't think it would work well on Mageia 3), though I can't guarantee that it will work.

Status: NEW => RESOLVED
Resolution: (none) => FIXED

I'm confused (nothing unusual ;)

[root@jackodesktop baz]# urpmi --debug ugene
getting lock on urpmi
parsing: /etc/urpmi/mediacfg.d/Devel-4-beta1-x86_64
parsing: /etc/urpmi/mediacfg.d/Devel-5-x86_64
examining synthesis file [/var/lib/urpmi/Core Release (zmrepo1)/synthesis.hdlist.cz]
examining synthesis file [/var/lib/urpmi/Core Updates (zmrepo3)/synthesis.hdlist.cz]
examining synthesis file [/var/lib/urpmi/Nonfree Release (zmrepo11)/synthesis.hdlist.cz]
examining synthesis file [/var/lib/urpmi/Nonfree Updates (zmrepo13)/synthesis.hdlist.cz]
examining synthesis file [/var/lib/urpmi/Tainted Release (zmrepo21)/synthesis.hdlist.cz]
examining synthesis file [/var/lib/urpmi/Tainted Updates (zmrepo23)/synthesis.hdlist.cz]
examining synthesis file [/var/lib/urpmi/Core 32bit Release (zmrepo31)/synthesis.hdlist.cz]
examining synthesis file [/var/lib/urpmi/Core 32bit Updates (zmrepo32)/synthesis.hdlist.cz]
examining synthesis file [/var/lib/urpmi/Nonfree 32bit Release (zmrepo36)/synthesis.hdlist.cz]
examining synthesis file [/var/lib/urpmi/Nonfree 32bit Updates (zmrepo37)/synthesis.hdlist.cz]
examining synthesis file [/var/lib/urpmi/Core Release Debug (distrib2)/synthesis.hdlist.cz]
getting exclusive lock on rpm
search_packages: found ugene-1.13.2-1.mga5.x86_64 matching ugene
found package(s): ugene-1.13.2-1.mga5.x86_64
opening rpmdb (root=, write=)
selecting ugene-1.13.2-1.mga5.x86_64
requiring libU2Algorithm.so.1()(64bit),libU2Core.so.1()(64bit),libU2Designer.so.1()(64bit),libU2Formats.so.1()(64bit),libU2Gui.so.1()(64bit),libU2Lang.so.1()(64bit),libU2Private.so.1()(64bit),libU2Remote.so.1()(64bit),libU2Script.so.1()(64bit),libU2Test.so.1()(64bit),libU2View.so.1()(64bit),libugenedb.so.1()(64bit) for ugene-1.13.2-1.mga5.x86_64
no packages match libU2Algorithm.so.1()(64bit) (it is either in skip.list or already rejected)
unselecting ugene-1.13.2-1.mga5.x86_64
adding a reason to already rejected package ugene-1.13.2-1.mga5.x86_64: unsatisfied libU2Algorithm.so.1()(64bit)
A requested package cannot be installed:
ugene-1.13.2-1.mga5.x86_64 (due to unsatisfied libU2Algorithm.so.1()(64bit))
Continue installation anyway? (Y/n) n
unlocking rpm database
unlocking urpmi database
EXITING (pid=30711)


[root@jackodesktop baz]# urpmf libU2Algorithm.so.1
    http://mtf.no-ip.co.uk/pub/linux/Mageia/distrib/cauldron/x86_64/media/core/release/media_info/20140503-225809-files.xml.lzma
ugene:/usr/libexec/ugene/libU2Algorithm.so.1                                                                                              
ugene:/usr/libexec/ugene/libU2Algorithm.so.1.0
ugene:/usr/libexec/ugene/libU2Algorithm.so.1.0.0
    http://mtf.no-ip.co.uk/pub/linux/Mageia/distrib/cauldron/x86_64/media/nonfree/release/media_info/20140503-161646-files.xml.lzma
    http://mtf.no-ip.co.uk/pub/linux/Mageia/distrib/cauldron/x86_64/media/tainted/release/media_info/20140503-151426-files.xml.lzma        
    http://mtf.no-ip.co.uk/pub/linux/Mageia/distrib/cauldron/i586/media/core/release/media_info/20140503-225538-files.xml.lzma             
ugene:/usr/libexec/ugene/libU2Algorithm.so.1                                                                                               
ugene:/usr/libexec/ugene/libU2Algorithm.so.1.0                                                                                             
ugene:/usr/libexec/ugene/libU2Algorithm.so.1.0.0                                                                                           
    http://mtf.no-ip.co.uk/pub/linux/Mageia/distrib/cauldron/i586/media/nonfree/release/media_info/20140503-161645-files.xml.lzma          
    http://distrib-coffee.ipsl.jussieu.fr/pub/linux/Mageia/distrib/cauldron/x86_64/media/debug/core/release/media_info/20140503-225603-files.xml.lzma                                                                                                                                 
ugene-debuginfo:/usr/lib/debug/usr/libexec/ugene/libU2Algorithm.so.1.0.0.debug                                                             
ugene-debuginfo:/usr/lib/debug/usr/libexec/ugene/libU2Algorithm.so.1.0.debug                                                               
ugene-debuginfo:/usr/lib/debug/usr/libexec/ugene/libU2Algorithm.so.1.debug
[root@jackodesktop baz]#

CC: (none) => zen25000

Thanks Barjac, indeed I noticed that the package was not working before I went to bed yesterday :-)

It seems that RPM lists ugene's libraries as requires, but since I put them in %{_libexecdir}, it can't find them. I'll try to put everything back to %{_libdir} for now, and I'll try to refine the package afterwards (the issue being that ugene puts everything in %{_libdir}: libraries, binaries, translations and data).

Status: RESOLVED => REOPENED
Resolution: FIXED => (none)

It works now :)

Status: REOPENED => RESOLVED
Resolution: (none) => FIXED

Yes confirmed.

Looks very clever, but I don't understand a word of it ;)

I like the watery graphic on the web page though - now that's impressive :)

Hi Rémi,

I am sorry for this really late reply (yes, I am a slow poke :-)). It
happened that I moved to Xubuntu pretty long ago and do not have any
Mageia installation, so unfortunately I am not able to test UGENE.
But anyway, this is a great news, because I am using UGENE heavily and
I'm sure many people working in biology/genomics/biophysics will love
it. Thank you!

Just out of curiosity - have you compiled it yourself or with the help
of its developers? I remember I contacted those Russian guys on their
support forum, but they were not too enthusiastic about making rpms for
Mageia or helping me to do that myself (though they had a couple of old
rmps for RH or Fedora). It is simpler in Ubuntu as they maintain their
own repository.

Once again, sorry for the late response and being not too much of help.

Best,

Grigory

P.S. Barry, a click on that watery graphics on the Help -> About will surprise you a bit too :-) Do you like Tetris? Good old classic Tetris? :-)