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Re: [Help] Test failures in q2-feature-classifier

Hi Étienne,

On Wed, Jan 27, 2021 at 07:58:51PM +0100, Étienne Mollier wrote:
> Your guess is right; setting the PYTHONPATH to the build
> directory allows most tests to run.  There were a couple of
> tests which then still failed to execute with the following
> symptom though:
> 	Command: vsearch --search_exact /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/q2_feature_classifier/tests/data/se-dna-sequences.fasta --id 0.8 --query_cov 0.8 --strand both --maxaccepts 10 --maxrejects 0 --db /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/q2_feature_classifier/tests/data/se-dna-sequences.fasta --threads 1 --output_no_hits --blast6out /tmp/tmpomuor76d
> 	----------------------------- Captured stderr call -----------------------------
> 	Fatal error: Invalid options to command search_exact
> 	Invalid option(s): --id --maxaccepts --maxrejects --query_cov
> 	The valid options for the search_exact command are: --alnout --biomout --blast6out --bzip2_decompress --db --dbmask --dbmatched --dbnotmatched --fasta_width --fastapairs --gzip_decompress --hardmask --log --match --matched --maxhits --maxqsize --maxqt --maxseqlength --maxsizeratio --maxsl --mincols --minqt --minseqlength --minsizeratio --minsl --mintsize --mismatch --mothur_shared_out --no_progress --notmatched --notrunclabels --otutabout --output_no_hits --qmask --quiet --relabel --relabel_keep --relabel_md5 --relabel_self --relabel_sha1 --rowlen --samheader --samout --self --sizein --sizeout --strand --threads --top_hits_only --uc --uc_allhits --userfields --userout --xee --xsize
> I believe this is not caught by upstream because their CI seems
> to stick to vsearch <= 2.7.0.  I could devise a patch to remove
> the use of invalid options with search_exact.  It is sufficient
> to enable the test suite to pass through and pushed changes to
> Salsa[1].  However I am unsure whether just skipping invalid
> options is the right way to go, or if there are some other
> options that might need setting instead.  Are there people at
> ease with vsearch use around ?

I think, if the test might pass without this option we could go with
this or even remove those tests temporarily and discuss the issue with
upstream without pressure of an open RC bug (which is unrelated).

As always: Thanks a lot for your work on this

> [1] https://salsa.debian.org/med-team/q2-feature-classifier


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