[Biojava-dev] Structures test failures

[Jules Jacobsen]

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fine it's probably just that you have an out-of date version of the 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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