[Bio-linux-dev] Fwd: Bio-Linux 7 package versions

[Tim Booth]

Hi Tony,

This isn't a mistake.  These package versions are correct.  The ones in
the archive really are older.  I've held off putting this new stuff in
the archive because as soon as I do (which will be very soon), Bio-Linux
6 users will start getting warnings that they can't upgrade these
packages due to dependency issues.  I could re-structure the archive to
avoid this but that entails extra work I don't want to do.

I've closed all the QIIME bugs I know about, and run some basic
regression tests which all passed.  If you have any more bugs please do
report them via Launchpad.  I should probably run a full regression test
using the official data but I've not got around to it yet.

Cheers,

TIM

On Thu, 2012-12-06 at 12:44 +0000, Tony Travis wrote:
> Hi, Tim.
> 
> I upgraded my laptop "beluga" from Bio-Linux 6 -> 7 using your script
> and everything seems to be working, but there are problems with some deb
> package versions. In particular, you seem to have omitted the 'epoch'
> for some new packages, making them look older than they are:
> 
> > root at beluga:~# apt-show-versions | grep -v uptodate
> > bio-linux-emboss 1:1bl1-1 newer than version in archive
> > bio-linux-estscan 2.1-12 newer than version in archive
> > bio-linux-mothur 2bl-5 newer than version in archive
> > bio-linux-paml 1:1bl1 newer than version in archive
> > bio-linux-prank 1:1bl1-1 newer than version in archive
> > bio-linux-rdp-classifier 2:1bl1-1 newer than version in archive
> > bio-linux-seaview 1:1bl1-1 newer than version in archive
> > bio-linux-transterm-hp 1:1bl1-1 newer than version in archive
> > bio-linux-trnascan 1:1bl1-1 newer than version in archive
> > bio-linux-wise2 1:1bl1-1 newer than version in archive
> 
> This is because the default 'epoch' is 0, and you put "1:" in the old
> Bio-Linux 6 deb version, but have omitted the 'epoch' in the newer
> Bio-Linux 7 version. For example:
> 
> > root at beluga:~# apt-cache policy bio-linux-emboss
> > bio-linux-emboss:
> >   Installed: 1:1bl1-1
> >   Candidate: 1:1bl1-1
> >   Version table:
> >  *** 1:1bl1-1 0
> >         100 /var/lib/dpkg/status
> >      6.3bl1-8 0
> >         500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
> 
> This can, of course, be resolved by forcing the correct version, but
> automatic upgrades will keep the 'newest' (i.e. epoch = 1:) version and
> not install the 'older' (default epoch = 0) version. I think this might
> expalin some of the problems with QIIME...
> 
> HTH,
> 
>    Tony.
> 
> 
> 
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-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705