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

[Andreas Tille]

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
> 
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