[Debian-med-packaging] Bug#960756: python-biopython FTBFS on 32bit: test_NCBI_BLAST_tools.BlastDB failures

[Peter Cock]

Perhaps makeblastdb itself failed (and our wrapper didn't notice)? Those
are the first files looked for after calling makeblastdb, to see if it
could make a BLAST database.  Are there any GenBank/NC_005816.fna.n* or
GenBank/NC_005816.faa.p* files present?

If it helps, the commands our script was trying to run were:

$ makeblastdb -dbtype nucl -in GenBank/NC_005816.fna \
-parse_seqids -hash_index -max_file_sz 20MB  -taxid 10

and:

$ makeblastdb -dbtype prot -in GenBank/NC_005816.faa \
-parse_seqids -hash_index -max_file_sz 20MB -taxid 10

I'm not sure I have remote access to any 32bit machines right now...

Peter

On Sat, May 16, 2020 at 2:22 PM Andreas Tille <andreas at an3as.eu> wrote:

> Control: tags -1 upstream
> Control: forwarded -1 Peter Cock <p.j.a.cock at googlemail.com>
>
> Hi Peter,
>
> it seems the patch applied does not work for 32bit architectures.
>
> Kind regards
>
>      Andreas.
>
> On Sat, May 16, 2020 at 02:25:20PM +0300, Adrian Bunk wrote:
> > Source: python-biopython
> > Version: 1.76+dfsg-2
> > Severity: serious
> > Tags: ftbfs
> >
> >
> https://buildd.debian.org/status/package.php?p=python-biopython&suite=sid
> >
> > ...
> > ======================================================================
> > FAIL: test_fasta_db_nucl (test_NCBI_BLAST_tools.BlastDB)
> > Test makeblastdb wrapper with nucleotide database.
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py",
> line 249, in test_fasta_db_nucl
> >     self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nhd"))
> > AssertionError: False is not true
> >
> > ======================================================================
> > FAIL: test_fasta_db_prot (test_NCBI_BLAST_tools.BlastDB)
> > Test makeblastdb wrapper with protein database.
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py",
> line 208, in test_fasta_db_prot
> >     self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phd"))
> > AssertionError: False is not true
> >
> > ----------------------------------------------------------------------
> > Ran 518 tests in 330.272 seconds
> >
> > FAILED (failures = 1)
> > Skipping any tests requiring internet access
> > Python version: 3.8.3 (default, May 14 2020, 11:03:12)
> > [GCC 9.3.0]
> > Operating system: posix linux
> > E: pybuild pybuild:352: test: plugin custom failed with: exit code=1:
> set -e; \
> >                              mkdir -p
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/home; \
> >                              mkdir -p
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc/examples; \
> >                              cp -a Doc/Tutorial.tex
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \
> >                              cp -a Doc/Tutorial
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \
> >                              cp -a Doc/examples
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \
> >                              cp -a Tests
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build; \
> >                              cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests; \
> >                              env DIALIGN2_DIR=/usr/share/dialign
> EMBOSS_ROOT=/usr/lib/emboss
> HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/home python3.8
> run_tests.py --offline
> > dh_auto_test: error: pybuild --test -i python{version} -p 3.8 --test
> --system=custom "--test-args=set -e; \\\
> >                              mkdir -p {build_dir}/home; \\\
> >                              mkdir -p {build_dir}/Doc/examples; \\\
> >                              cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\
> >                              cp -a Doc/Tutorial {build_dir}/Doc; \\\
> >                              cp -a Doc/examples {build_dir}/Doc; \\\
> >                              cp -a Tests {build_dir}; \\\
> >                              cd {build_dir}/Tests; \\\
> >                              env DIALIGN2_DIR=/usr/share/dialign
> EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter}
> run_tests.py --offline" returned exit code 13
> > make[1]: *** [debian/rules:83: override_dh_auto_test] Error 25
> >
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at alioth-lists.debian.net
> >
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
>
> --
> http://fam-tille.de
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20200516/533ddb1f/attachment.html>