[Biojava-dev] Unit test error

[Richard Holland]

Looks like not all the biojava JAR files (bytecode.jar, etc.) are on
your classpath when you run the test. This message appears about
halfway through your stacktrace:

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


cheers,
Richard

2008/9/13 Zainul Franciscus <zainul_irfandhy at yahoo.com.sg>:
> 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
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/