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

[Andreas Tille]

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



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