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Re: Bug#937606: Droping Python2 support for Biopython

On Sat, Dec 21, 2019 at 07:41:53AM +0200, Graham Inggs wrote:
> > I've read that it is blocked due to the Python3.8 transition.  If you
> > ask me this transition looks like not happening in the next 10 days
> > since several packages are looking like they would need some time.
> python-biopython is prevented from migrating by at least seqsero and srst2.

The versions in unstable are depending python3-biopython.  The packages are
not migrating due to

   seqsero/i386 unsatisfiable Depends: sra-toolkit  [1]


   Invalidated by dependency            [2]
   Invalidated by build-dependency
   Build-Depends(-Arch): srst2 bowtie2 (not considered)
   Depends: srst2 bowtie2 (not considered)

For the latter I wonder how bowtie can be helped to migrate since
the build log[3] says:

./bowtie2-build --large-index --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -F 10,1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp  .simple_tests.gz
E: Build killed with signal TERM after 150 minutes of inactivity

This is the same for all "slow" architectures and I wonder whether we
should exclude this test for certain architectures.  A bit suspicious
is s390x[4] which has a different issue which might need investigation.

Kind regards


[1] https://qa.debian.org/excuses.php?package=seqsero
[2] https://qa.debian.org/excuses.php?package=srst2
[3] https://buildd.debian.org/status/fetch.php?pkg=bowtie2&arch=i386&ver=
[4] https://buildd.debian.org/status/fetch.php?pkg=bowtie2&arch=s390x&ver=


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