[Debian-med-packaging] Bug#956324: python-biopython: FTBFS on mipsel

[Peter Cock]

I agree this is most likely a clustalo error. I think the first two
examples use
temporary input files created during the Biopython tests. However, the third
failing example ought to be useful in isolation:

clustalo -i Fasta/f002 --guidetree-out temp_test.dnd -o temp_test.aln
--outfmt clustal --force

The input file is here (plain text with no extension):

https://github.com/biopython/biopython/blob/master/Tests/Fasta/f002

Peter

On Fri, Apr 10, 2020 at 6:29 AM Andreas Tille <tille at debian.org> wrote:

> Control: forwarded -1 Peter Cock <p.j.a.cock at googlemail.com>
>
> Hi Peter,
>
> the log that is linked to below says in the end:
>
>
> ======================================================================
> ERROR: test_input_filename_with_space
> (test_ClustalOmega_tool.ClustalOmegaTestNormalConditions)
> Test an input filename containing a space.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py",
> line 175, in test_input_filename_with_space
>     self.standard_test_procedure(cline)
>   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py",
> line 63, in standard_test_procedure
>     output, error = cline()
>   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/Application/__init__.py",
> line 530, in __call__
>     raise ApplicationError(return_code, str(self),
> Bio.Application.ApplicationError: Non-zero return code 138 from 'clustalo
> -i "Clustalw/temp horses.fasta" -o temp_test.aln --outfmt clustal --force',
> message 'Bus error'
>
> ======================================================================
> ERROR: test_large_fasta_file
> (test_ClustalOmega_tool.ClustalOmegaTestNormalConditions)
> Test a large fasta input file.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py",
> line 210, in test_large_fasta_file
>     self.standard_test_procedure(cline)
>   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py",
> line 63, in standard_test_procedure
>     output, error = cline()
>   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/Application/__init__.py",
> line 530, in __call__
>     raise ApplicationError(return_code, str(self),
> Bio.Application.ApplicationError: Non-zero return code 138 from 'clustalo
> -i temp_cw_prot.fasta -o temp_cw_prot.aln --outfmt clustal --force',
> message 'Bus error'
>
> ======================================================================
> ERROR: test_newtree_files
> (test_ClustalOmega_tool.ClustalOmegaTestNormalConditions)
> Test requesting a guide tree.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py",
> line 224, in test_newtree_files
>     self.standard_test_procedure(cline)
>   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py",
> line 63, in standard_test_procedure
>     output, error = cline()
>   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/Application/__init__.py",
> line 530, in __call__
>     raise ApplicationError(return_code, str(self),
> Bio.Application.ApplicationError: Non-zero return code 138 from 'clustalo
> -i Fasta/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt
> clustal --force', message 'Bus error'
>
> ----------------------------------------------------------------------
>
>
> I'm not sure whether you have any clue about this since it looks rather
> like a clustalo issue - but I guess you could be interested.  Please let
> us know what you think about this.
>
> Kind regards
>
>        Andreas.
>
> On Thu, Apr 09, 2020 at 10:38:04PM +0200, Sebastian Ramacher wrote:
> > Source: python-biopython
> > Version: 1.76+dfsg-1
> > Severity: serious
> > Tags: ftbfs sid bullseye
> > Justification: fails to build from source (but built successfully in the
> past)
> >
> > python-biopython failed to build on mipsel:
> >
> https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=mipsel&ver=1.76%2Bdfsg-1%2Bb1&stamp=1586419338&raw=0
> >
> > Cheers
> > --
> > Sebastian Ramacher
>
>
>
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at alioth-lists.debian.net
> >
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>
>
> --
> http://fam-tille.de
>
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