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 <andr...@an3as.eu> wrote: > Control: tags -1 upstream > Control: forwarded -1 Peter Cock <p.j.a.c...@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-packag...@alioth-lists.debian.net > > > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging > > -- > http://fam-tille.de >