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

[Tony Travis]

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.