Hi,
On 04/13/2018 10:36 AM, Michael Crusoe wrote: > > 2018-04-13 16:00 GMT+03:00 Chris Hofstaedtler <[email protected] > <mailto:[email protected]>>: > > * Michael Crusoe <[email protected] > <mailto:[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? > FYI, my machine has 4 cores and the tests are passing here. Cheers.
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