[BioRuby] Running BioRuby tests offline

[Naohisa GOTO]

Hi Peter,

The proposal is marked as a Feature Request to BioRuby.
https://redmine.open-bio.org/issues/3293

Thanks,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 15 Sep 2011 20:17:57 +0100
Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Hi all,
> 
> I recently tried running the BioRuby test suite while offline (on a train),
> 
> 
> $ ruby runner.rb
> Loaded suite .
> Started
> ...............F.........EE.....EEEEEEEEFFEFEEEFEE...EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEFFFFFFFFFFFFFFFFFFFE.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 .
>  !
>  ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FF.............................................................................................................................
 .!
>  
>  ......................................................................
> ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 .
>  !
>  ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
> Finished in 100.74387 seconds.
> 
>   1) Failure:
> test_read_uri(Bio::FuncTestCommandNet) [./functional/bio/test_command.rb:337]:
> Exception raised:
> Class: <SocketError>
> Message: <"getaddrinfo: nodename nor servname provided, or not known">
> ---Backtrace---
> ...
>  73) Failure:
> test_libxml(Bio::TestPhyloXML_Check_LibXML) [./unit/bio/db/test_phyloxml.rb:29]:
> Error: libxml-ruby library is not present. Please install libxml-ruby
> library. It is needed for Bio::PhyloXML module. Unit test for PhyloXML
> will not be performed.
> <nil> is not true.
> 
> 3640 tests, 20824 assertions, 26 failures, 47 errors
> 
> By eye, all 73 failures or errors were down to missing the XML
> library, or lacking network access.
> 
> Is there a way to run the test suite skipping the tests requiring
> network access?
> 
> If BioRuby starts running nightly tests (I was talking to Raoul about
> this at the BioHackathon last month), an offline switch would seem a
> good idea. We do this in Biopython to avoid hitting any online servers
> too hard, and because network issues would otherwise get flagged as
> potential regressions (false positives).
> 
> Regards,
> 
> Peter
> 
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