<div dir="ltr">I agree this is most likely a clustalo error. I think the first two examples use<div>temporary input files created during the Biopython tests. However, the third</div><div>failing example ought to be useful in isolation:</div><div><br></div><div>clustalo -i Fasta/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force</div><div><br></div><div>The input file is here (plain text with no extension):</div><div><br></div><div><a href="https://github.com/biopython/biopython/blob/master/Tests/Fasta/f002">https://github.com/biopython/biopython/blob/master/Tests/Fasta/f002</a><br><div><br></div><div>Peter<br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Apr 10, 2020 at 6:29 AM Andreas Tille <<a href="mailto:tille@debian.org">tille@debian.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Control: forwarded -1 Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>><br>
<br>
Hi Peter,<br>
<br>
the log that is linked to below says in the end:<br>
<br>
<br>
======================================================================<br>
ERROR: test_input_filename_with_space (test_ClustalOmega_tool.ClustalOmegaTestNormalConditions)<br>
Test an input filename containing a space.<br>
----------------------------------------------------------------------<br>
Traceback (most recent call last):<br>
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py", line 175, in test_input_filename_with_space<br>
self.standard_test_procedure(cline)<br>
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py", line 63, in standard_test_procedure<br>
output, error = cline()<br>
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/Application/__init__.py", line 530, in __call__<br>
raise ApplicationError(return_code, str(self),<br>
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'<br>
<br>
======================================================================<br>
ERROR: test_large_fasta_file (test_ClustalOmega_tool.ClustalOmegaTestNormalConditions)<br>
Test a large fasta input file.<br>
----------------------------------------------------------------------<br>
Traceback (most recent call last):<br>
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py", line 210, in test_large_fasta_file<br>
self.standard_test_procedure(cline)<br>
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py", line 63, in standard_test_procedure<br>
output, error = cline()<br>
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/Application/__init__.py", line 530, in __call__<br>
raise ApplicationError(return_code, str(self),<br>
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'<br>
<br>
======================================================================<br>
ERROR: test_newtree_files (test_ClustalOmega_tool.ClustalOmegaTestNormalConditions)<br>
Test requesting a guide tree.<br>
----------------------------------------------------------------------<br>
Traceback (most recent call last):<br>
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py", line 224, in test_newtree_files<br>
self.standard_test_procedure(cline)<br>
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_ClustalOmega_tool.py", line 63, in standard_test_procedure<br>
output, error = cline()<br>
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/Application/__init__.py", line 530, in __call__<br>
raise ApplicationError(return_code, str(self),<br>
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'<br>
<br>
----------------------------------------------------------------------<br>
<br>
<br>
I'm not sure whether you have any clue about this since it looks rather<br>
like a clustalo issue - but I guess you could be interested. Please let<br>
us know what you think about this.<br>
<br>
Kind regards<br>
<br>
Andreas.<br>
<br>
On Thu, Apr 09, 2020 at 10:38:04PM +0200, Sebastian Ramacher wrote:<br>
> Source: python-biopython<br>
> Version: 1.76+dfsg-1<br>
> Severity: serious<br>
> Tags: ftbfs sid bullseye<br>
> Justification: fails to build from source (but built successfully in the past)<br>
> <br>
> python-biopython failed to build on mipsel:<br>
> <a href="https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=mipsel&ver=1.76%2Bdfsg-1%2Bb1&stamp=1586419338&raw=0" rel="noreferrer" target="_blank">https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=mipsel&ver=1.76%2Bdfsg-1%2Bb1&stamp=1586419338&raw=0</a><br>
> <br>
> Cheers<br>
> -- <br>
> Sebastian Ramacher<br>
<br>
<br>
<br>
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<br>
<br>
-- <br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
</blockquote></div>