Hi,

On 04/13/2018 10:36 AM, Michael Crusoe wrote:
>
> 2018-04-13 16:00 GMT+03:00 Chris Hofstaedtler <z...@debian.org
> <mailto:z...@debian.org>>:
>
>     * Michael Crusoe <michael.cru...@gmail.com
>     <mailto:michael.cru...@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?
>  

FYI, my machine has 4 cores and the tests are passing here.

Cheers.




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