[BioRuby] test and bioruby shell questions

[Ben Woodcroft]

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



2008/8/31 Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp>:
> Hi,
>
> On Sat, 30 Aug 2008 21:13:32 +1000
> "Ben Woodcroft" <donttrustben at gmail.com> wrote:
>
>> Hi,
>>
>> Using the edge version of bioruby I get 7 errors as well, although
>> they are slightly different. I wouldn't be too worried.
>
> What BioRuby version, Ruby version, and OS and CPU did you use?
>
>>
>> $ ruby runner.rb
>> Loaded suite .
>> Started
>> .....FF..F..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
>  .!
>>  ..............................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
>> Finished in 133.52153 seconds.
>>
>  1) Failure:
> test_gff_exportview(Bio::FuncTestEnsemblHuman)
> [./functional/bio/io/test_ensembl.rb:95]:
> (snip)
>
> 1) to 3) seems the same as the previous mail.
> http://rubyforge.org/tracker/index.php?func=detail&aid=21744&group_id=769&atid=3037
> This still remains unfixed.
>
>>   4) Failure:
>> test_id_line_sequence_version(Bio::TestEMBL)
>> [./unit/bio/db/embl/test_embl_rel89.rb:45]:
>> <"1"> expected but was
>> <nil>.
>
> I see this first time.
> Which bioruby version?
>
>>   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 believe commit 735e3563b723645afa65f0e4213a7c92152f68ec
> fixed 5) to 7).
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



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