[BioRuby] test and bioruby shell questions

[Ben Woodcroft]

Hi,

Your commits seem to fix things, as I only get the first 3 errors. Thanks
again,
ben

$ ruby runner.rb
Loaded suite .
Started
.....FF..F........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Finished in 141.782259 seconds.

  1) Failure:
test_gff_exportview(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:95]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  2) Failure:
test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:121]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  3) Failure:
test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:180]:
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tENSG00000206158\tENST00000382964\tENSE00001494097\tKNOWN_protein_coding\n">
expected but was
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n">.

1906 tests, 4111 assertions, 3 failures, 0 errors


2008/9/1 Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp>

> Hi Ben,
>
> The failures 4) to 7) may be caused by the conflicts of test class names.
> I changed test class names to fix this.
> (commits 536cdf903a3c3908c117efd554d33117d91452f4 and
> 0fe1e7d3ed02185632f4a34d8efe1f21f755b289).
>
> Current HEAD is:
>
> http://github.com/bioruby/bioruby/commit/0fe1e7d3ed02185632f4a34d8efe1f21f755b289
>
> Note that the first three failures are still unfixed.
>
> Could you please try again?
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
> On Sun, 31 Aug 2008 17:11:31 +1000
> "Ben Woodcroft" <donttrustben at gmail.com> wrote:
>
> > Hi,
> >
> > Thanks for your concern.
> > After pulling from the newest github -
> >
> http://github.com/bioruby/bioruby/commit/e86f8d757c45805389e154f06ccde5a3d9e8a557
> >
> > $ ruby -v
> > ruby 1.8.6 (2007-09-24 patchlevel 111) [i486-linux]
> > $ uname -a
> > Linux uyen 2.6.24-21-generic #1 SMP Mon Aug 25 17:32:09 UTC 2008 i686
> GNU/Linux
> >
> > Using Ubuntu Hardy, and the latest patched version of the ruby1.8
> > package (1.8.6.111-2ubuntu1.1)
> >
> > $ ruby runner.rb
> > Loaded suite .
> > Started
> >
> .....FF..F..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
>  .!
> >
>  ..............................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
> > Finished in 142.816902 seconds.
> >
> >   1) Failure:
> > test_gff_exportview(Bio::FuncTestEnsemblHuman)
> > [./functional/bio/io/test_ensembl.rb:95]:
> > <"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
> > transcript_id=ENST00000382964; exon_id=ENSE00001494097;
> > gene_type=KNOWN_protein_coding\n"> expected but was
> > <"">.
> >
> >   2) Failure:
> > test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
> > [./functional/bio/io/test_ensembl.rb:121]:
> > <"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
> > transcript_id=ENST00000382964; exon_id=ENSE00001494097;
> > gene_type=KNOWN_protein_coding\n"> expected but was
> > <"">.
> >
> >   3) Failure:
> > test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
> > [./functional/bio/io/test_ensembl.rb:180]:
> >
> <"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tENSG00000206158\tENST00000382964\tENSE00001494097\tKNOWN_protein_coding\n">
> > expected but was
> >
> <"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n">.
> >
> >   4) Failure:
> > test_id_line_sequence_version(Bio::TestEMBL)
> > [./unit/bio/db/embl/test_embl_rel89.rb:45]:
> > <"1"> expected but was
> > <nil>.
> >
> >   5) Failure:
> > test_left_padding(Bio::TestStringFormatting)
> > [./unit/bio/util/restriction_enzyme/test_string_formatting.rb:43]:
> > <"nnnnnnn"> expected but was
> > <"">.
> >
> >   6) Failure:
> > test_right_padding(Bio::TestStringFormatting)
> > [./unit/bio/util/restriction_enzyme/test_string_formatting.rb:50]:
> > <"nn"> expected but was
> > <"">.
> >
> >   7) Error:
> > test_strip_padding(Bio::TestStringFormatting):
> > NoMethodError: undefined method `[]' for nil:NilClass
> >     ../lib/bio/util/restriction_enzyme/string_formatting.rb:64:in
> > `strip_padding'
> >     ./unit/bio/util/restriction_enzyme/test_string_formatting.rb:33:in
> > `test_strip_padding'
> >
> > 1867 tests, 4049 assertions, 6 failures, 1 errors
> >
> > I don't actually care personally about these problems, but am glad to
> > help out in a general sense.
> >
> > Thanks,
> > ben
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> BioRuby at lists.open-bio.org
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