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 <[email protected]> wrote: > Control: forwarded -1 Peter Cock <[email protected]> > > 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 > > [email protected] > > > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging > > > -- > http://fam-tille.de >
