[BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org

[Peter Cock]

2011/11/1 Tiago Antão <tiagoantao at gmail.com>:
> 2011/11/1 Tiago Antão <tiagoantao at gmail.com>:
>> On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO
>> <ngoto at gen-info.osaka-u.ac.jp> wrote:
>>>  % ruby test/runner.rb
>>
>> I run with this and now it works fine: ie reports an error. The error
>> is just that I do not have the XML parser installed.
>> Please see:
>> http://testing.open-bio.org/bioruby/waterfall

Is the XML dependency optional? In Biopython we skip tests
where a optional dependency is missing (i.e. report this but
don't count it as a failure).

>
> Is anyone interested in receiving emails with errors? Should I send
> them to the list? At this initial stage I would recommend sending to a
> just few developers...
>
> There is now a potential real error:
>  1) Failure:
> test_convert(Bio::FuncTestTogoWSREST)
> [./test/functional/bio/io/test_togows.rb:120]:
> Exception raised:
> Class: <Errno::EINVAL>
> Message: <"Invalid argument - connect(2)">
> ---Backtrace---
> /usr/lib/ruby/1.8/net/http.rb:560:in `initialize'
> /usr/lib/ruby/1.8/net/http.rb:560:in `open'
> /usr/lib/ruby/1.8/net/http.rb:560:in `connect'
> /usr/lib/ruby/1.8/timeout.rb:53:in `timeout'
> /usr/lib/ruby/1.8/timeout.rb:101:in `timeout'
> /usr/lib/ruby/1.8/net/http.rb:560:in `connect'
> /usr/lib/ruby/1.8/net/http.rb:553:in `do_start'
> /usr/lib/ruby/1.8/net/http.rb:542:in `start'
> /usr/lib/ruby/1.8/net/http.rb:1035:in `request'
> /usr/lib/ruby/1.8/net/http.rb:845:in `post'
> ./lib/bio/command.rb:702:in `http_post_form'
> ./lib/bio/io/togows.rb:414:in `post_data'
> ./lib/bio/io/togows.rb:305:in `convert'
> ./test/functional/bio/io/test_togows.rb:121:in `test_convert'
> ./test/functional/bio/io/test_togows.rb:120:in `test_convert'

That's a TogoWS test using the network to
connect the Togo Web Service (I have some
similar tests and code ready for Biopython now).
I can't tell you if the problem is in BioRuby, the
network, or TogoWS though.

Peter