Another issue in test suite of new version of bioperl.

[Carnë Draug]

On Wed, 6 Feb 2019 at 12:27, Andreas Tille <tille at debian.org> wrote:
>
> Hi Carnė,
>
> On Tue, Feb 05, 2019 at 04:53:44PM +0000, Carnė Draug wrote:
> >
> > There was a bug on the test for requires_networking.  It should be
> > fixed on the 1.7.4 version that was released today.
>
> Thanks for the pointer - uploaded yesterday.  Any solution for the
> issue with bioperl-run (#921495)?
>

I replied on the bug tracker for that specific issue.

But please read the Change file of the release.  There has been a
*lot* of changes on the last release.  There's almost no bug fix, it's
all about removing modules, removing programs, adding new modules from
other distributions, and dropping dependencies.

One very nice change is that this release breaks the circular
dependence on bioperl-run (bioperl was dependent on bioperl-run which
the was dependent on bioperl)

Many of the modules removed were moved into separate distributions.
But while there's a repository for those new distributions, upstream
has not actually made releases.

Also, note that in CPAN, this is the BioPerl distribution.  In Debian
there's the bioperl source package, the debian bioperl binary package
(scripts from that package), and libbio-perl-perl (the perl modules).
However:

    1) the BioPerl distribution no longer has the Bio::Perl module so
    the name libbio-perl-perl would no longer be a good match.

    2) upstream does not consider bioperl to be the scripts.  The
    scripts are just a secondary thing.  BioPerl main thing are the
    modules.  And with the split of bioperl into smaller modules,
    there is also bioperl the project which would be all of the
    bioperl distributions.