[Biojava-dev] Structures test failures

[Steve Darnell]

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