Re: Request for sponsorship: ruby-crb-blast

2018-04-13 16:00 GMT+03:00 Chris Hofstaedtler <zeha@debian.org>:

* Michael Crusoe <michael.crusoe@gmail.com> [180413 14:30]:
> Due to a bug the binary package was deleted in unstable which is blocking
> me as a DM from uploading the new version:

Had a quick look, but on my 4-core machine the tests are failing,
snippet of one:

Thanks for checking!

test: crb-blast should not find fake scaffold name. : E
===============================================================================
Error: test: crb-blast should not find fake scaffold name. (TestCRBBlast):
RuntimeError: BLAST Error:
USAGE
blastx [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-max_intron_length length] [-seg SEG_options]
[-soft_masking soft_masking] [-matrix matrix_name]
[-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-comp_based_stats compo] [-use_sw_tback] [-version]

DESCRIPTION
Translated Query-Protein Subject BLAST 2.7.1+

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Argument "num_threads". Illegal value, expected (>=1 and =<4): `6'
Error: (CArgException::eConstraint) Argument "num_threads". Illegal value, expected (>=1 and =<4): `6'
/<<PKGBUILDDIR>>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:214:in `run_blast_with_threads'
/<<PKGBUILDDIR>>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:173:in `run_blast'

I assume this is caused by your fewer-threads patch :)

Strange, this behaviour is explictly fixed by https://salsa.debian.org/ruby-team/ruby-crb-blast/blob/master/debian/patches/test_less_threads

Looks like I missed a couple other examples, so I pushed another commit. Does that fix it for you?