[Debian-med-packaging] Bug#939894: Minia is lacking symbol from gatb-core (Was: Bug#939894: minia: autopkgtest regression: X.contigs.fa: No such file or directory)

[Andreas Tille]

On Mon, Sep 09, 2019 at 09:59:09PM +0200, Paul Gevers wrote:
> ************ Run simple_test.sh ****************
> Traceback (most recent call last):
>   File "compare_fasta.py", line 21, in <module>
>     s2 = read_seqs(fasta2)
>   File "compare_fasta.py", line 15, in read_seqs
>     for  line in open(fasta):
> IOError: [Errno 2] No such file or directory: 'X.contigs.fa'

The actual problem is:

   $ /usr/bin/minia
/usr/bin/minia: symbol lookup error: /usr/bin/minia: undefined symbol: _ZN4gatb4core8debruijn4impl9link_tigsILm128EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiRmb

I suspect minia needs a different / newer version of libgatbcore2.

@Olivier: You once said you have contact to gatb-core upstream and their
downstream projects.  Would you be able to teach them about a sensible
release strategy with some API the depending projects could rely on?  As
far as I can see the depending projects rely on Git submodules with a
specific commit which is not really helpful.

Kind regards

        Andreas.

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