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=all=0.6.9-1=1520009847=0
>
> ...
> ┌──┐
> │ Run tests for ruby2.3 from debian/ruby-tests.rake
> │
> └──┘
>
> RUBYLIB=/<>/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
> /<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:348:
> warning: shadowing outer local variable - name
> /<>/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
> /<>/test/test_test3.rb:28: warning: assigned but unused variable
> - blaster
> /<>/test/test_test3.rb:44: warning: assigned but unused variable
> - dbs
> /<>/test/test_test3.rb:45: warning: assigned but unused variable
> - run
> /<>/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'
/<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:214:in
`run_blast_with_threads'
/<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:173:in
`run_blast'
/<>/test/test_test.rb:14:in `block (2 levels) in
'
===
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
