[DRE-maint] Bug#892066: ruby-crb-blast FTBFS: test failures

[Adrian Bunk]

On Sun, Mar 04, 2018 at 10:35:15PM +0200, Adrian Bunk wrote:
> Source: ruby-crb-blast
> Version: 0.6.9-1
> Severity: serious
> 
> https://buildd.debian.org/status/fetch.php?pkg=ruby-crb-blast&arch=all&ver=0.6.9-1&stamp=1520009847&raw=0
> 
> ...
> ┌──────────────────────────────────────────────────────────────────────────────┐
> │ Run tests for ruby2.3 from debian/ruby-tests.rake                            │
> └──────────────────────────────────────────────────────────────────────────────┘
> 
> RUBYLIB=/<<PKGBUILDDIR>>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby:. GEM_PATH=debian/ruby-crb-blast/usr/share/rubygems-integration/all:/var/lib/gems/2.3.0:/usr/lib/x86_64-linux-gnu/rubygems-integration/2.3.0:/usr/share/rubygems-integration/2.3.0:/usr/share/rubygems-integration/all ruby2.3 -S rake -f debian/ruby-tests.rake
> /usr/bin/ruby2.3 -w -I"test"  "/usr/lib/ruby/vendor_ruby/rake/rake_test_loader.rb" "test/test_test.rb" "test/test_bin.rb" "test/test_test.rb" "test/test_test2.rb" "test/test_test3.rb" -v
> /<<PKGBUILDDIR>>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:348: warning: shadowing outer local variable - name
> /<<PKGBUILDDIR>>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:348: warning: shadowing outer local variable - seq
> /usr/lib/ruby/vendor_ruby/fixwhich.rb:3: warning: assigned but unused variable - e
> /usr/lib/ruby/vendor_ruby/threach.rb:7: warning: `*' interpreted as argument prefix
> /usr/lib/ruby/vendor_ruby/threach.rb:13: warning: shadowing outer local variable - i
> /<<PKGBUILDDIR>>/test/test_test3.rb:28: warning: assigned but unused variable - blaster
> /<<PKGBUILDDIR>>/test/test_test3.rb:44: warning: assigned but unused variable - dbs
> /<<PKGBUILDDIR>>/test/test_test3.rb:45: warning: assigned but unused variable - run
> /<<PKGBUILDDIR>>/test/test_test3.rb:46: warning: assigned but unused variable - load
> Loaded suite /usr/lib/ruby/vendor_ruby/rake/rake_test_loader
> Started
> Test2CRBBlast: 
>   test: crb-blast should add secondary hits. :		E
> ===============================================================================
> Error: test: crb-blast should add secondary hits. (Test2CRBBlast):
>   RuntimeError: BLAST Error:
>   USAGE
>     blastn [-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] [-perc_identity float_value]
>       [-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] [-penalty penalty] [-reward reward] [-no_greedy]
>       [-min_raw_gapped_score int_value] [-template_type type]
>       [-template_length int_value] [-dust DUST_options]
>       [-filtering_db filtering_database]
>       [-window_masker_taxid window_masker_taxid]
>       [-window_masker_db window_masker_db] [-soft_masking soft_masking]
>       [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
>       [-best_hit_score_edge float_value] [-window_size int_value]
>       [-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
>       [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
>       [-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]
>       [-version]
>   
>   DESCRIPTION
>      Nucleotide-Nucleotide BLAST 2.7.1+

I omitted the relevant part of the log in the following lines:


  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'
/<<PKGBUILDDIR>>/test/test_test.rb:14:in `block (2 levels) in <class:TestCRBBlast>'
===============================================================================


cu
Adrian

-- 

       "Is there not promise of rain?" Ling Tan asked suddenly out
        of the darkness. There had been need of rain for many days.
       "Only a promise," Lao Er said.
                                       Pearl S. Buck - Dragon Seed