[Biojava-dev] Structures test failures

[Scooter Willis]

Jules

I am not having in problem with Netbeans 6.9 with the latest patches. I do like the improved debug GUI in 6.9 for inspecting collections. I haven't done a fresh install of 6.9.1.

Scooter

On Aug 24, 2010, at 8:41 AM, Jules Jacobsen wrote:

> Hi Steve,
> 
> Unless you're a staunch Eclipse user I can recommend Netbeans for maven 
> as it works very well with it. One issue I've had is that Netbeans 6.9 
> is generally slower and more cumbersome than 6.8, worse still 6.9.1 
> seems incapable of connecting to the repository at all. So stick with 
> 6.8 and it should be fine.
> 
> I can confirm that the most recent dev version of biojava-structure does 
> not fail any tests, although I just tried checking out the read-only 
> public version from svn://code.open-bio.org/biojava/biojava-live/trunk 
> and encountered a 'rev-props' error and now I'm unable to connect at all...
> 
> Your error isn't likely to be maven related - if everything else ran 
> fine it's probably just that you have an out-of date version of the 
> source as the structure module is independent of the other modules, but 
> I can't tell for sure without seeing the error messages produced by the 
> failed tests.
> 
> Regards,
> 
> Jules
> 
> On 23/08/2010 17:21, Steve Darnell wrote:
>> Greetings,
>> 
>> 
>> 
>> I am attempting to build biojava from the anonymous svn server at
>> github; I cannot even connect to the anonymous svn server at open-bio.
>> I am unable to package/install the structure module and I suspect it is
>> caused by two failures that occur in the unit tests:
>> 
>> 
>> 
>> Failed tests:
>> 
>>   testOldSecOutput(org.biojava.bio.structure.TestSECalignment)
>> 
>>   testParsePairs(org.biojava.bio.structure.align.TestAlignDBSearchPairs)
>> 
>> 
>> 
>> Tests run: 61, Failures: 2, Errors: 0, Skipped: 0
>> 
>> 
>> 
>> The build log has no indication that the structure module was packaged
>> or installed.
>> 
>> 
>> 
>> I have yet to configure Eclipse to build biojava, so this is how I
>> attempted to build it on the command line:
>> 
>> 
>> 
>> $ svn co http://svn.github.com/biojava/biojava.git ./biojava
>> 
>> $ cd biojava
>> 
>> $ mvn clean install>  biojava.log&  tail -f biojava.log
>> 
>> $ cd ~/.m2/repository/org/biojava
>> 
>> $ ls
>> 
>> % alignment
>> 
>> % biojava
>> 
>> % biojava3-alignment
>> 
>> % biojava3-core
>> 
>> % biojava3-phylo
>> 
>> % blast
>> 
>> % bytecode
>> 
>> % core
>> 
>> 
>> 
>> I am new to maven, so it is likely I am overlooking something obvious.
>> I have reproduced this outcome on OSX 10.6.4 and Ubuntu 10.04.  I would
>> appreciate any suggestions that the dev list might have.
>> 
>> 
>> 
>> Best regards,
>> 
>> Steve Darnell
>> 
>> 
>> 
>> 
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