[Bio-linux-dev] Tophat/Cufflinks, Ubuntu Quantal and libboost dependency

[Booth, Timothy G.]

Hi Pierre,

I hope you don't mind me copying this to the developers mailing list.

The boost libraries are a bit weird as they have the version number as part of the package name, meaning that libboost-thread1.49.0 can never satisfy libboost-thread1.48.0 because APT sees them as completely different packages.  There was definitely some fundamental incompatibility between 1.46 and 1.48 that necessitated them doing this but I don't know if this applies to 1.49 or if it is just a hang over.  If it is, I could relax the dependencies so that the packages will install for you.  But it may be that the packages compiled with 1.48 really do need 1.48 and separate package builds are needed on Quantal.

As I'm out of the office this week it will be a little while before I can send you modified packages to try.  If you want to get your hands dirty and try rebuilding the DEBs yourself you can find some brief pointers here:

http://www.debian.org/doc/manuals/apt-howto/ch-sourcehandling.en.html

You'll need to modify debian/control and debian/changelog in the unpacked source directory before rebuilding.

Cheers,

TIM
________________________________________
From: Pierre POUCHIN [pierre.pouchin at udamail.fr]
Sent: 29 March 2013 16:38
To: Booth, Timothy G.
Subject: Tophat/Cufflinks, Ubuntu Quantal and libboost dependency

Good afternoon Mr Booth,

Recently, my lab bought a server on which we’d like to install Galaxy and other bioinformatics tools.
We installed Ubuntu 12.10 on this server and discovered the bio-linux ppa from which I tried to install packages – although we know it is for Ubuntu 12.04...

However, I encountered a dependency problem related to libboost-thread:

tophat : Depends: libboost-thread1.48.0 (>= 1.48.0-1) but it is not installable
cufflinks : Depends: libboost-thread1.48.0 (>= 1.48.0-1) but it is not installable

I don’t understand this problem, since 12.10 provides libboost-thread1.49.0 which should satisfy the requirements…
It’s as if the dependency is more an “==” than a “>=”. Is it an expected behavior ?

I hope I did not miss something obvious…

In any case, thank you for your repository.


Best regards,

Pierre Pouchin,
Research associate

Laboratoire GReD,
UMR/CNRS6293, Clermont Université, INSERM U1103
Faculté de Médecine, 28 Place H. Dunant
63000 Clermont-Ferrand
France

Tel: (33) (0)4 73 17 81 92



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