[BioRuby] Bioruby unit tests

Christian M Zmasek czmasek at burnham.org
Fri Jun 12 21:13:13 UTC 2009


Hi:

I usually have one test fail (I don't remember which one though) but not 
that many.
Which version of ruby are you using?

Christian


Diana Jaunzeikare wrote:
> Hi all,
>
> I am working on implementing phyloxml support and I was running only 
> my unit tests to test my code. Then yesterday I ran all of the unit 
> tests and it gave me errors (when I first cloned it did not gave me 
> any errors). I don't think i changed anything in any other file than 
> lib/bio/db/phyloxml.rb and test/unit/bio/db/test_phyloxml.rb
>
> Here is the output of test/runner.rb. Looks all of the errors are of 
> the same kind. 
>
> diana at diana-ubuntu:~/bioruby$ ruby test/runner.rb
> Loaded suite .
> Started
> .........................................................................................EE...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................EE........................................................................................................................................................................................................................................EEEEEE...................................................................E........E.................................................................................................................................................................EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE.................................................................................................................................................................................................................................................................................................................................................................................................................................................EEEEEE...............................................................................................................................
> Finished in 176.329241 seconds.
>
>   1) Error:
> test_output_embl(Bio::FuncTestSequenceOutputEMBL):
> ArgumentError: wrong number of arguments (1 for 0)
>     ./lib/bio/sequence.rb:263:in `initialize'
>     ./lib/bio/sequence.rb:263:in `new'
>     ./lib/bio/sequence.rb:263:in `auto'
>     ./test/functional/bio/sequence/test_output_embl.rb:21:in `setup'
>
>   2) Error:
> test_output_fasta(Bio::FuncTestSequenceOutputEMBL):
> ArgumentError: wrong number of arguments (1 for 0)
>     ./lib/bio/sequence.rb:263:in `initialize'
>     ./lib/bio/sequence.rb:263:in `new'
>     ./lib/bio/sequence.rb:263:in `auto'
>     ./test/functional/bio/sequence/test_output_embl.rb:21:in `setup'
>
>   3) Error:
> test_alignment(Bio::TestAlignmentMultiFastaFormat):
> ArgumentError: wrong number of arguments (1 for 0)
>     ./lib/bio/sequence.rb:443:in `initialize'
>     ./lib/bio/sequence.rb:443:in `new'
>     ./lib/bio/sequence.rb:443:in `adapter'
>     ./lib/bio/db/fasta.rb:221:in `to_seq'
>     ./lib/bio/appl/mafft/report.rb:90:in `determine_seq_method'
>     ./lib/bio/appl/mafft/report.rb:89:in `each'
>     ./lib/bio/appl/mafft/report.rb:89:in `determine_seq_method'
>     ./lib/bio/appl/mafft/report.rb:61:in `alignment'
>     ./test/unit/bio/appl/mafft/test_report.rb:47:in `test_alignment'
>
>   4) Error:
> test_determine_seq_method(Bio::TestAlignmentMultiFastaFormat):
> ArgumentError: wrong number of arguments (1 for 0)
>     ./lib/bio/sequence.rb:443:in `initialize'
>     ./lib/bio/sequence.rb:443:in `new'
>     ./lib/bio/sequence.rb:443:in `adapter'
>     ./lib/bio/db/fasta.rb:221:in `to_seq'
>     ./lib/bio/appl/mafft/report.rb:90:in `determine_seq_method'
>     ./lib/bio/appl/mafft/report.rb:89:in `each'
>     ./lib/bio/appl/mafft/report.rb:89:in `determine_seq_method'
>     ./lib/bio/appl/mafft/report.rb:61:in `alignment'
>     ./test/unit/bio/appl/mafft/test_report.rb:57:in 
> `test_determine_seq_method'
>
>   5) Error:
> test_const_version(Bio::TestGFF3):
> ArgumentError: wrong number of arguments (1 for 0)
>     ./lib/bio/sequence.rb:443:in `initialize'
>     ./lib/bio/sequence.rb:443:in `new'
>     ./lib/bio/sequence.rb:443:in `adapter'
>     ./lib/bio/db/fasta.rb:221:in `to_seq'
>     ./lib/bio/db/gff.rb:954:in `parse_fasta'
>     ./lib/bio/db/gff.rb:949:in `each_line'
>     ./lib/bio/db/gff.rb:949:in `parse_fasta'
>     ./lib/bio/db/gff.rb:941:in `parse'
>     ./lib/bio/db/gff.rb:881:in `initialize'
>     ./test/unit/bio/db/test_gff.rb:644:in `new'
>     ./test/unit/bio/db/test_gff.rb:644:in `setup'
>
>   6) Error:
> test_gff_version(Bio::TestGFF3):
> ArgumentError: wrong number of arguments (1 for 0)
>     ./lib/bio/sequence.rb:443:in `initialize'
>     ./lib/bio/sequence.rb:443:in `new'
>     ./lib/bio/sequence.rb:443:in `adapter'
>     ./lib/bio/db/fasta.rb:221:in `to_seq'
>     ./lib/bio/db/gff.rb:954:in `parse_fasta'
>     ./lib/bio/db/gff.rb:949:in `each_line'
>     ./lib/bio/db/gff.rb:949:in `parse_fasta'
>     ./lib/bio/db/gff.rb:941:in `parse'
>     ./lib/bio/db/gff.rb:881:in `initialize'
>     ./test/unit/bio/db/test_gff.rb:644:in `new'
>     ./test/unit/bio/db/test_gff.rb:644:in `setup'
>
>   7) Error:
> test_records(Bio::TestGFF3):
> ArgumentError: wrong number of arguments (1 for 0)
>     ./lib/bio/sequence.rb:443:in `initialize'
>     ./lib/bio/sequence.rb:443:in `new'
>     ./lib/bio/sequence.rb:443:in `adapter'
>     ./lib/bio/db/fasta.rb:221:in `to_seq'
>     ./lib/bio/db/gff.rb:954:in `parse_fasta'
>     ./lib/bio/db/gff.rb:949:in `each_line'
>     ./lib/bio/db/gff.rb:949:in `parse_fasta'
>     ./lib/bio/db/gff.rb:941:in `parse'
>     ./lib/bio/db/gff.rb:881:in `initialize'
>     ./test/unit/bio/db/test_gff.rb:644:in `new'
>     ./test/unit/bio/db/test_gff.rb:644:in `setup'
>
>   8) Error:
> test_sequence_regions(Bio::TestGFF3):
> ArgumentError: wrong number of arguments (1 for 0)
>     ./lib/bio/sequence.rb:443:in `initialize'
>     ./lib/bio/sequence.rb:443:in `new'
>     ./lib/bio/sequence.rb:443:in `adapter'
>     ./lib/bio/db/fasta.rb:221:in `to_seq'
>     ./lib/bio/db/gff.rb:954:in `parse_fasta'
>     ./lib/bio/db/gff.rb:949:in `each_line'
>     ./lib/bio/db/gff.rb:949:in `parse_fasta'
>     ./lib/bio/db/gff.rb:941:in `parse'
>     ./lib/bio/db/gff.rb:881:in `initialize'
>     ./test/unit/bio/db/test_gff.rb:644:in `new'
>     ./test/unit/bio/db/test_gff.rb:644:in `setup'
> [....]
> 2175 tests, 5180 assertions, 0 failures, 54 errors
>
>
> Any ideas?  Code is available here 
> http://github.com/latvianlinuxgirl/bioruby/tree/dev
>  
> Diana






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