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

[Tim Booth]

Hi Tony,

You're right, except that there is no upstream for these packages as
they are not built from the source packages at all...

My reasoning is that these packages have been converted from ones that
contain the actual application to wrappers that depend on the native
Debian packages (either from upstream or from the PPA).  So
bio-linux-emboss 1:1bl1-1 is actually wrapper package v1 that pulls in
the real EMBOSS version whatever.  I've deliberately taken the EMBOSS
version out of there as the wrapper wraps emboss+jemboss+embassy and
these all have different versions, and I don't want to have to manually
update the wrapper version every time I update EMBOSS.

The proper Debian packages within the PPA all have proper versions that
match the upstream, so if you see anything like '1bl1' in the version
you need to check out the real package it wraps.

I know that the -1 extension indicates a non-native package but I
started calling them bl1, bl2 etc. until I realised that bl10 sorts
before bl2.  At that point I just gave up and went with bl1-1.

Clear as mud?

On Wubi, I've made a decision that I don't have time to look at it
myself but I know many users would be grateful to have it running if you
are able to take it on.

Cheers,

TIM

> I don't understand your package versions:
> 
> bio-linux-emboss 1:1bl1-1 means	epoch = 1, upstream = 1bl1, deb = 1
> bio-linux-emboss 6.3bl1-8 means	epoch = 0, upstream = 6.3bl1, deb = 8
> 
> I posted to the list because that looks like upstream 6.3bl1 is newer 
> than upstream 1bl1 to me. Have I got that wrong?
> 
> > 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.
> 
> Drat, that means all our NBX's are going to be broken: Well, maybe it's 
> time to upgrade them to Bio-Linux 7 anyway :-)
> 
> > 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.
> 
> OK, I'll report anything I find + I'll take a look at Wubi too.
> 
> Bye,
> 
>    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