[Biojava-dev] Unit test error

[Andy Yates]

Hi Zainul,

This isn't an issue specific to running Biojava tests on Linux  
(Biojava developers work on a variety of platforms including Windows,  
Linux & Mac). The real problem here is framework is unable to find the  
AlphabetManager.xml file on your classpath. From the root of the  
biojava source tree it is located in:

resources/org/biojava/bio/symbol/AlphabetManager.xml

Try adding the resources directory to your Eclipse build path & try  
again.

Regards,

Andy

On 13 Sep 2008, at 12:43, Zainul Franciscus wrote:

> Dear All,
>
> I got this exception when I ran the unit test for :
> org 
> .biojavax 
> .ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver. Here  
> is my environment specification:
>
> IDE: Eclipse 3.2
> JRE: java-1.5.0-gcj-1.5.0.0
> OS: Ubuntu 8.04 (Hardy Heron)
>
> Does any one ever run Biojava in Linux environment ? I suspect that  
> this
> error is because of the JRE. Has anyone been successful in running
> biojava in ubuntu before ? If yes may I know your eclipse JRE  
> setting ?
>
> Thank you.
>
> Regards,
> Zainul Franciscus
>
>
> Stack trace:
>
> org.biojava.bio.BioError: Unable to initialize DNATools
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at
> org 
> .biojavax 
> .ga 
> .functions 
> .SimpleCrossOverFunctionTest 
> .testPerformCrossOver(SimpleCrossOverFunctionTest.java:56)
>   at java.lang.reflect.Method.invoke(libgcj.so.81)
>   at junit.framework.TestCase.runTest(TestCase.java:168)
>   at junit.framework.TestCase.runBare(TestCase.java:134)
>   at junit.framework.TestResult$1.protect(TestResult.java:110)
>   at junit.framework.TestResult.runProtected(TestResult.java:128)
>   at junit.framework.TestResult.run(TestResult.java:113)
>   at junit.framework.TestCase.run(TestCase.java:124)
>   at junit.framework.TestSuite.runTest(TestSuite.java:232)
>   at junit.framework.TestSuite.run(TestSuite.java:227)
>   at
> org 
> .junit 
> .internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:81)
>   at
> org 
> .eclipse 
> .jdt 
> .internal 
> .junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:38)
>   at
> org 
> .eclipse 
> .jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
>   at
> org 
> .eclipse 
> .jdt 
> .internal 
> .junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:460)
>   at
> org 
> .eclipse 
> .jdt 
> .internal 
> .junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)
>   at
> org 
> .eclipse 
> .jdt 
> .internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)
>   at
> org 
> .eclipse 
> .jdt 
> .internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java: 
> 196)
> Caused by: org.biojava.bio.BioError: Couldn't locate
> AlphabetManager.xml.  This probably means that your biojava.jar file  
> is
> corrupt or incorrectly built.
>   at
> org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java: 
> 150)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:79)
>   ...18 more
>
>
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