[BioRuby] Travis-CI & bundler problem
Joachim Baran
joachim.baran at gmail.com
Thu Nov 7 17:13:45 UTC 2013
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
>
>
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