2018-04-13 16:00 GMT+03:00 Chris Hofstaedtler <[email protected]>: > * Michael Crusoe <[email protected]> [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? > > Chris > > -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/> Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania https://orcid.org/0000-0002-2961-9670 <https://impactstory.org/u/0000-0002-2961-9670> [email protected] +1 480 627 9108
