Bug#921495: Bioperl 1.7.4 should not migrate to Buster

[Andreas Beckmann]

On 28/11/2019 11.05, Michael Crusoe wrote:
> Would breaks+replaces libbio-perl-run-perl (<<1.7.3) make sense?

Exactly.

Andreas

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

[Michael Crusoe]

Thanks Andreas Beckmann!

Would breaks+replaces libbio-perl-run-perl (<<1.7.3) make sense?

On Thu, Nov 28, 2019 at 12:00 AM Andreas Beckmann  wrote:

> Followup-For: Bug #921495
> Control: found -1 1.7.6-1
>
> libbio-perl-perl is missing proper
>   Breaks+Replaces: libbio-perl-run-perl (<< 1.7.3)
>
> There is a typoed (lib?io-perl-run-perl) and wrongly versioned
>   Breaks: libio-perl-run-perl (<= 1.7.3-1), roary (<= 3.12.0+dfsg-2)
> without corresponding Replaces. (Without the typo it would break the
> 'fixed' version in sid, too.)
> And (<< 1.7.3-1) would be wrong, too, since it hits a potential
> 1.7.3-1~bpo10+1
>
> Also the broken version of roary is likely wrong: you most likely want
>   roary (<< 3.13)
> (just think of a buster-pu upload of roary 3.12.0+dfsg-2+deb10u1).
>
>
> Andreas
>
>

-- 
Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project

https://orcid.org/-0002-2961-9670

m...@commonwl.org
+1 480 627 9108

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

[Andreas Beckmann]

Followup-For: Bug #921495
Control: found -1 1.7.6-1

libbio-perl-perl is missing proper
  Breaks+Replaces: libbio-perl-run-perl (<< 1.7.3)

There is a typoed (lib?io-perl-run-perl) and wrongly versioned
  Breaks: libio-perl-run-perl (<= 1.7.3-1), roary (<= 3.12.0+dfsg-2)
without corresponding Replaces. (Without the typo it would break the
'fixed' version in sid, too.)
And (<< 1.7.3-1) would be wrong, too, since it hits a potential
1.7.3-1~bpo10+1

Also the broken version of roary is likely wrong: you most likely want
  roary (<< 3.13)
(just think of a buster-pu upload of roary 3.12.0+dfsg-2+deb10u1).


Andreas

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

[Andreas Beckmann]

Followup-For: Bug #921495
Control: found -1 1.7.5-1

There is a file overwrite issue upgrading from buster:

  Preparing to unpack .../libbio-perl-perl_1.7.5-1_all.deb ...
  Unpacking libbio-perl-perl (1.7.5-1) over (1.7.2-3) ...
  dpkg: error processing archive 
/var/cache/apt/archives/libbio-perl-perl_1.7.5-1_all.deb (--unpack):
   trying to overwrite '/usr/share/man/man3/Bio::Tools::Run::Analysis.3pm.gz', 
which is also in package libbio-perl-run-perl 1.7.2-4
  dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)
  Errors were encountered while processing:
   /var/cache/apt/archives/libbio-perl-perl_1.7.5-1_all.deb


Andreas


libbio-perl-run-perl=1.7.2-4_libbio-perl-perl=1.7.5-1.log.gz
Description: application/gzip

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

[Andreas Tille]

On Mon, Feb 11, 2019 at 04:15:21PM +, Carnë Draug wrote:
> > 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

Done
 
> but should add this new one (already packaged):
> 
>   libbio-tools-run-alignment-clustalw

Arggg, no idea why I missed this in my upload.  Just added in Git.

Thanks for all your hints

  Andreas.

-- 
http://fam-tille.de

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

[Carnë Draug]

On Mon, 11 Feb 2019 at 15:47, Andreas Tille  wrote:
>
> On Mon, Feb 11, 2019 at 03:32:47PM +, 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

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

[Andreas Tille]

On Mon, Feb 11, 2019 at 03:32:47PM +, 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?

Kind regards

  Andreas.

-- 
http://fam-tille.de

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

[Carnë Draug]

On Mon, 11 Feb 2019 at 14:06, Andreas Tille  wrote:
>
> Hi Carnė,
>
> On Mon, Feb 11, 2019 at 12:59:45PM +, Carnė Draug wrote:
> > On Wed, 6 Feb 2019 at 14:06, Andreas Tille  wrote:
> > > This is what I've though about: Removing the files from bioperl-run
> > > (which would be 1.7.2-5 then)
> >
> > Upstream has released BioPerl-Run 1.7.3 which fixes this conflict
> > issue.  If someone could prepare that release that would be nice.
>
> Thanks a lot for this hint.
>
> > Like BioPerl 1.7.3, this new release of BioPerl-Run removed multiple
> > modules and so, probably not suitable for migration to Buster during
> > this transition freeze period.
>
> This is demonstrated very well here:
>
> https://tracker.debian.org/pkg/bioperl
>
> Lots of packages (not only bioperl-run) are broken by the new version.

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.

> 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?

Thank you
David

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

[Andreas Tille]

Hi Carnë,

On Mon, Feb 11, 2019 at 12:59:45PM +, Carnë Draug wrote:
> On Wed, 6 Feb 2019 at 14:06, Andreas Tille  wrote:
> > This is what I've though about: Removing the files from bioperl-run
> > (which would be 1.7.2-5 then)
> 
> Upstream has released BioPerl-Run 1.7.3 which fixes this conflict
> issue.  If someone could prepare that release that would be nice.

Thanks a lot for this hint.
 
> Like BioPerl 1.7.3, this new release of BioPerl-Run removed multiple
> modules and so, probably not suitable for migration to Buster during
> this transition freeze period.

This is demonstrated very well here:

https://tracker.debian.org/pkg/bioperl

Lots of packages (not only bioperl-run) are broken by the new version.
Thus I admit I see no real profit in upgrading bioperl-run at this
release stage.  We could upload to experimental (Carnë, 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.

For sure everybody is invited to fix all those packages in experimental
that are currently broken by bioperl 1.7.4.  This would enable a smooth
transition after testing is open for Buster+1.

Kind regards

   Andreas.

-- 
http://fam-tille.de