[BioRuby] Bioruby unit tests

Fri Jun 12 21:23:35 UTC 2009

I am using

ruby 1.8.7 (2008-08-11 patchlevel 72) [i486-linux]

Diana

On Fri, Jun 12, 2009 at 5:13 PM, Christian M Zmasek <czmasek at burnham.org>wrote:

> 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
>>
>
>
>