[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)

[Olivier Sallou]

On 9/12/19 10:11 AM, Andreas Tille wrote:
> 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.
unfortunatly, there is nobody left in my lab related to this software... :-(
>
> Kind regards
>
>         Andreas.
>
-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

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