[Debian-med-packaging] Bug#921495: Bioperl 1.7.4 should not migrate to Buster

[Carnë Draug]

On Mon, 11 Feb 2019 at 15:47, Andreas Tille <tille at debian.org> wrote:
>
> On Mon, Feb 11, 2019 at 03:32:47PM +0000, Carnë Draug wrote:
> >
> > Well, all those regressions are because they can't install bioperl
> > which is their dependency.  There is no issue on themselves or in
> > upstream bioperl.  The issue is that Debian's bioperl claims to have
> > recommend dependency on bioperl-run which does not actually exist in
> > upstream anymore.
>
> OK.
>
> > > Thus I admit I see no real profit in upgrading bioperl-run at this
> > > release stage.  We could upload to experimental (Carnė, I'm explicitly
> > > encouraging you to do so if you have some interest in it).  I for
> > > myself have currently more important things on my desk since this
> > > becomes important for my only after Buster release.
> >
> > I'm not interested on bioperl-run either.  But can you remove the
> > current bioperl from sid which is causing all those issues on the
> > other packages?
>
> There is no easy way to remove a package from sid.  The only way would
> be to upload version 1.7.2 with an epoch (1:1.7.2).  Since epochs are
> ugly I would like to avoid this.  If it hurds anybody to much we might
> consider uploading bioperl-run as well.  Since it probably needs a
> versioned depends ob bioperl 1.7.4 it should not migrate to testing as
> well.  But since all these regressions are only in sid I see no real
> harm (except Ubuntu might fetch from unstable and will end up with
> broken bioperl stuff.
>
> What do you think?

All packages that depend on bioperl are being affected by this.  The
current situation is a bit awkward because packaging and testing in
sid fails even though it would be fine in testing.  This will cause
issues for new releases of such packages and for false positives in
Debian's ci.

If you do make a new bioperl-run release, you can drop the following
dependencies:

  bowtie
  bwa
  maq
  paml
  t-coffee

but should add this new one (already packaged):

  libbio-tools-run-alignment-clustalw

David