Hello, I had a quick look at the test suite of python-biopython. Currently, my impression is that most warnings spawning during the test are normal, and more or less related to data or functions being stressed. The following warning message: test_lowess ... /usr/lib/python3/dist-packages/Bio/Statistics/__init__.py:11: BiopythonDeprecationWarning: Bio.Statistics has been deprecated, and we intend to remove it in a future release of Biopython. is caused by: >>> from Bio.Statistics.lowess import lowess which is the (deprecated) module being tested. The following warning: test_SeqIO_Insdc ... /build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank/Scanner.py:304: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)? originates from the test data, looking non-standardly formatted on purpose: FT CDS join(1..100,101..110 FT ) FT /protein_id="Test" FT /db_xref="PEDANT:PE04150000123" This variant does not complain, but might miss the point of the test as well (upstream measures tests coverage): FT CDS join(1..100,101..110) FT /protein_id="Test" FT /db_xref="PEDANT:PE04150000123" Similarly, the next few messages mainly seem caused by the nature of test data: test_codonalign ... /build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Bio/Seq.py:2713: BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be translated as amino acid. test_PDB_StructureAlignment ... /build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298. warnings.warn( /build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344. The test against NCBI BLAST tools might be more concerning, the following warning is outputted several times in a row: test_NCBI_BLAST_tools ... /build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:481: UserWarning: NCBI BLAST+ blastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) But this seems more or less related to this github issue: https://github.com/biopython/biopython/issues/2184 It is curious as it occurs with makeblastdb 2.10.0, but maybe I understood the issue the other way around. Kind Regards, -- Étienne Mollier <etienne.mollier@mailoo.org> Fingerprint: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d Help find cures against the Covid-19 ! Give CPU cycles: * Rosetta@home: https://boinc.bakerlab.org/rosetta/ * Folding@home: https://foldingathome.org/
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