[BioRuby] Travis-CI & bundler problem

[Iain Barnett]

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