[BioRuby] test and bioruby shell questions

[Naohisa GOTO]

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