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Old 07-02-2011, 11:11 PM   #1
yaximik
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Question I am puzzled...help!


He all,

I am trying to install bioinformatics package ugene1.9.3 on SL55 (RHEL55), which among other things requires qt-devel >= 4.5.0. From Qt website I tried to install Qt SDK 1.1.2 that includes Qt Libraries 4.7.3, etc. However, installer reports Missing dependency: /usr/lib/libstdc++.so.6 is needed for...
However, libstdc++.so.6 is present as link to libstdc++.so.6.0.8 in both /usr/lib/ and /usr/lib64/ ! What is the problem then? Please advise.
 
Old 07-02-2011, 11:25 PM   #2
divyashree
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Quote:
Originally Posted by yaximik View Post
He all,

I am trying to install bioinformatics package ugene1.9.3 on SL55 (RHEL55), which among other things requires qt-devel >= 4.5.0. From Qt website I tried to install Qt SDK 1.1.2 that includes Qt Libraries 4.7.3, etc. However, installer reports Missing dependency: /usr/lib/libstdc++.so.6 is needed for...
However, libstdc++.so.6 is present as link to libstdc++.so.6.0.8 in both /usr/lib/ and /usr/lib64/ ! What is the problem then? Please advise.
Install the exact version of the QT that is required. Here ugene1.9.3 requires QT devel version 4.5 but you installed 4.7 . So it will give dependency error.
 
Old 07-03-2011, 12:39 AM   #3
yaximik
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Well, I did not even get to installation of ugene1.9.3, since Qt SDK failed to instal becasue of missing dependency. How do I tell the system that I have the missing library?
 
Old 07-03-2011, 12:54 AM   #4
Sjonnie48
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Quote:
I am trying to install bioinformatics package ugene1.9.3 on SL55 (RHEL55)
It's obvious that you've arrived in dependency-hell!
Did you select this package from an official repository for your distribution/version?
I guess not because in such case all dependencies would have been solved.
 
Old 07-03-2011, 02:01 AM   #5
divyashree
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Quote:
Originally Posted by yaximik View Post
Well, I did not even get to installation of ugene1.9.3, since Qt SDK failed to instal becasue of missing dependency. How do I tell the system that I have the missing library?
You should install QT from your SL repository or install it from 3rd part repository like rpmfprge.
 
Old 07-03-2011, 02:11 AM   #6
Tinkster
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Quote:
Originally Posted by yaximik View Post
Well, I did not even get to installation of ugene1.9.3, since Qt SDK failed to instal becasue of missing dependency. How do I tell the system that I have the missing library?
Have you considered looking at centos repos for actual
RPMs of Qt you may be able to use for this?


http://rpm.pbone.net/index.php3/stat...earch/qt-devel


Cheers,
Tink
 
Old 07-03-2011, 04:21 AM   #7
knudfl
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Suggest : The Pramberger repo
http://www.pramberger.at/peter/services/repository/
( You will also find "qt47 pramberger" in the link from @Tinkster.)
http://plone.lucidsolutions.co.nz/li...rpm-repository
# wget -q -O- "http://devel.pramberger.at/getrepo?release=5" >> /etc/yum.repos.d/pramberger.repo


Probably : # yum remove qt4-devel

And then : # yum install qt47-devel.x86_64 qt47-demo.x86_64

..

Last edited by knudfl; 07-03-2011 at 05:19 AM.
 
Old 07-03-2011, 08:31 AM   #8
knudfl
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Ugene-1.9.3 seems to be buggy.
( There is a package for Fedora 16. So obviously it can be build.)

Version 1.9.1 compiles OK on EL5 / SL55, 64bits with qt47-*.
The command 'ugene -ui' opens the GUI.
( I found that 1.9.1 is the latest version available for Ubuntu,
when I searched for patches for Debian, Fedora. ( No patches found)).

The compile test was done with the source ugene_1.9.1+repack :
http://ftp.klid.dk/ftp/ubuntu/pool/universe/u/ugene/
http://ftp.klid.dk/ftp/ubuntu/pool/u...ck.orig.tar.gz
> ugene_1.9.1+repack.orig.tar.gz : 14-Feb-2011.

..
 
Old 07-03-2011, 04:47 PM   #9
yaximik
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Thnakms everyone for taking time trying to help. After long investigating it appears that problem with libstdc++ missing dependency is quite widespread and discussed a lot on the net with other installations. It generally boils down to situations when people trying to use rpms compiled for close, but not the same OS. So inmy case, ugene1.9.3 installers are for Fedora and Ubuntu, but not for SL55/RHEL55.

So I got its source and tried to rebuild rpm, an got the same result - needs qt>=4.5.0. Since I already failed with installation of qt4.7 package, I got from archives qt-all-opensource-src-4.5.3, the closest to what is needed. I got it recompiled and installed - I presume, since I can run included qtdemo. However, rebuilding of ugene1.9.3 still demands qt-devel>=4.5.0.

pirut showed that bunch of qt-3.3.6* are present or even installed, but nothing about 4.5.3 I just installed. Well, this may be becasue I did not use rpm to install qt4.5.3.

I have uninstalled anything related to qt3.3.6. The qtdemo (from 4.5.3 installation) still runs, so I presume qt4.5.3 is intalled - how do I check it otherwise? And how to tell ugene1.9.3 that qt>=4.5.0 is in fact present and functional?

I try to follow knudfl's advice - thanks!
 
Old 07-03-2011, 07:39 PM   #10
yaximik
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Thanks, knudfl! I got qt47-devel installed and it shows as installed after search for installed gt in pirut. I got ugene1.9.1 installation running just using instructions in profided in build.txt - which did not work at all with 1.9.3. However, watching make output I see that it uses qt-4.5.3 I installed earlier, but not gt47-*. I guess it is because somewhere qt-4.5* is expected, but not gt47-*. Again, I can see qt47-* installed in pirut, but not qt4.5.3 - is there another way to check what is installed if rpm or yum was not used?
 
Old 07-03-2011, 08:08 PM   #11
knudfl
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When you type : 'qmake -r', the qmake that is first in the PATH, will be used.

And I guess, you can find out, if the used qmake was connected to
/usr/lib64/qt4/bin/qmake or /usr/lib64/qt47/bin/qmake. Or another one ?

The qt4* used at compile time will also be used at run time.
( But : It doesn't really matter, as ugene should compile with both.)

Quote:
I guess it is because somewhere qt-4.5* is expected, but not gt47-*
Not correct, qt-4.5 or later is the requirement.

Quote:
- is there another way to check what is installed if rpm or yum was not used?
The standard way of checking for installed rpm packages ( qt ) is :
'rpm -qa | grep qt'.
A manual install can (only) be traced with 'find' or 'locate'.

..
 
  


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