[BioRuby] Travis-CI & bundler problem

[Joachim Baran]

Hi!

  Thanks for putting work into this!

  So, you are getting rspec to fail on your local machine? That is
interesting, because I might have some file lingering around on my machine
that makes it work for me then!

Joachim



On 7 November 2013 11:48, Iain Barnett <iainspeed at gmail.com> wrote:

>
> On 7 Nov 2013, at 16:03, Joachim Baran wrote:
>
> Hi!
>
> On 7 November 2013 10:20, Iain Barnett <iainspeed at gmail.com> wrote:
>
>> How long do the specs normally take to run for you? I started them a
>> while ago (using Ruby v2) and they seem to be stuck, which would indicate
>> to me that I may end up with a blown stack.
>>
>   Normally the tests run for a little bit over a minute. The current tests
> that have the stack problem (not all of them have it) fail in under a
> minute.
>
>
>> Can you post a link to one of these so I can see what you mean about it
>> being a TravisCI problem?
>>
>   I have not done too much research into this, but I got the impression
> that it is a set-up problem on TravisCI's side by reading through the
> comments of this report: http://jira.codehaus.org/browse/JRUBY-6203
>
> Joachim
>
>
> I've changed some of the specs and code around and now I can get the specs
> to run, but I get a failure and also a stack level error, using v1.9.3.
> I've pushed the changes to
> https://github.com/yb66/BioInterchange/tree/rspec-changes.
>
> It's quite possible I've broken something with my changes - especially for
> 1.8, which I've not run this against - but there's nothing that should be
> fundamental though as I've not touched the workings of the library, just
> the way it loads. Let me know if you see anything wrong since you know the
> code a lot better, and I'll change it and try again.
>
>
> I get the following output on running rspec:
>
> <snip>
>
> BioInterchange::Phylogenetics::CDAORDFWriter
>   serialization of tree models
>     Given an empty document
>       should be zero
>     Given a single Newick tree
>       should eq 103 (FAILED - 1)
>
> <snip>
>
> BioInterchange::TextMining::RDFWriter
>   serialization of text-mining documents
>     empty document
>     document with two entities (FAILED - 2)
>     full advanced json document (FAILED - 3)
>
> Failures:
>
>   1) BioInterchange::Phylogenetics::CDAORDFWriter serialization of tree
> models Given a single Newick tree
>      Failure/Error: it { should eq 103 }
>
>        expected: 103
>             got: 0
>
>        (compared using ==)
>      # ./spec/phylogenetics_spec.rb:79:in `block (4 levels) in <top
> (required)>'
>
>   2) BioInterchange::TextMining::RDFWriter serialization of text-mining
> documents document with two entities
>      Failure/Error: Unable to find matching line from backtrace
>      SystemStackError:
>        stack level too deep
>      #
> /Users/iainuser/RubyProjects/BioInterchange/vendor/ruby/2.0.0/gems/rdf-1.0.10.1/lib/rdf/query/pattern.rb:36
>
>   3) BioInterchange::TextMining::RDFWriter serialization of text-mining
> documents full advanced json document
>      Failure/Error: Unable to find matching line from backtrace
>      SystemStackError:
>        stack level too deep
>      #
> /Users/iainuser/RubyProjects/BioInterchange/vendor/ruby/2.0.0/gems/rdf-1.0.10.1/lib/rdf/query/pattern.rb:36
>
>
>
> Regards,
> Iain
>
>