Re: Seqan2 FTBFS
On Wed, 2022-12-07 at 14:07 +0200, Andrius Merkys wrote:
> Hello,
>
> On 2022-12-07 10:02, olivier sallou wrote:> Is it really failing ?
> [1]
> link only shows failure due to max execution
> > time in CI and job was killed by CI.
>
> seqan2 indeed builds (it takes many hours on single CPU on
> barriere.d.o), but fails most of its tests with the following:
>
> a bytes-like object is required, not 'str' <class 'TypeError'>
this is a classic error when switching from python2 to python3...
so tests should be updated to work with python3... or be dropped as
python2 only....
>
> I gave a quick glance at 'app_test_yara':
>
> $ /usr/bin/python3
> "/home/merkys/seqan2-2.4.0+dfsg/apps/yara/tests/run_tests.py"
> "/home/merkys/seqan2-2.4.0+dfsg"
> "/home/merkys/seqan2-2.4.0+dfsg/obj-x86_64-linux-gnu"
> Executing test for Yara
> ==============================
>
> /home/merkys/seqan2-2.4.0+dfsg/obj-x86_64-linux-gnu/bin/yara_indexer
> /home/merkys/seqan2-2.4.0+dfsg/apps/yara/tests/input/adeno-genome.fa
> -o
> /tmp/tmpb51ofmfz/adeno-genome OK
> Error when trying to compare
> /home/merkys/seqan2-2.4.0+dfsg/apps/yara/tests/gold/adeno-
> reads_1.t1.sam
> to /tmp/tmpb51ofmfz/adeno-reads_1.t1.sam: a bytes-like object is
> required, not 'str' <class 'TypeError'>
> /home/merkys/seqan2-2.4.0+dfsg/obj-x86_64-linux-gnu/bin/yara_mapper
> /home/merkys/seqan2-2.4.0+dfsg/apps/yara/tests/gold/adeno-genome
> /home/merkys/seqan2-2.4.0+dfsg/apps/yara/tests/input/adeno-reads_1.fa
> -o
> /tmp/tmpb51ofmfz/adeno-reads_1.t1.sam --threads 1 FAILED
> DELETING TEMP DIR /tmp/tmpb51ofmfz
> ==============================
> total tests: 2
> failed tests: 1
> successful tests: 1
> ==============================
>
> It seems that one of the required output files is not produced. Any
> idea
> why?
>
> Andrius
> > > [1]https://salsa.debian.org/med-team/seqan2/-/jobs/3622896
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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