[BioRuby] Bioruby unit tests

[Diana Jaunzeikare]

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