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+
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