[BioRuby] test and bioruby shell questions

[Naohisa GOTO]

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