[Biojava-dev] test failures on biojava/biojava git repo

[Michael Heuer]

Hello Andreas,

>From command line, OSX 10.6.8, JDK 1.6, maven 3.0.4

$ mvn -version
Apache Maven 3.0.4 (r1232337; 2012-01-17 02:44:56-0600)
Maven home: /Users/xxx/bin/maven-latest
Java version: 1.6.0_31, vendor: Apple Inc.
Java home: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Default locale: en_US, platform encoding: MacRoman
OS name: "mac os x", version: "10.6.8", arch: "x86_64", family: "mac"


It fails from the top level multimodule build and also from inside the
biojava3-genome module.

   michael


On Tue, Aug 7, 2012 at 6:51 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Michael,
>
> Works fine for me on linux and osx.  Are you doing this from command
> line or an IDE? Can you verify that the src/test/resources directory
> is on your project build path? -
>
> - besides this, agreed that this should be using a tmp file rather
> than creating files at that location.
>
> Andreas
>
> On Tue, Aug 7, 2012 at 8:15 AM, Michael Heuer <heuermh at gmail.com> wrote:
>> Hello,
>>
>> Thought I would try working with the git mirrors today but
>> unfortunately biojava/biojava git repo fails unit tests for me on OSX
>>
>> -------------------------------------------------------
>>  T E S T S
>> -------------------------------------------------------
>> Running org.biojava3.genome.GeneFeatureHelperTest
>> Aug 7, 2012 10:03:18 AM org.biojava3.genome.parsers.gff.GFF3Reader read
>> INFO: Gff.read(): Reading src/test/resources/amphimedon.gff3
>> Gene EDEN found at ctgA 1050 9000 POSITIVE
>> Gene rna-Apple3 found at ctgA 18000 21200 POSITIVE
>> Aug 7, 2012 10:03:18 AM org.biojava3.genome.parsers.gff.GFF3Reader read
>> INFO: Gff.read(): Reading
>> /Users/mheuer/working/biojava-git/biojava3-genome/src/test/resources/volvox.gff3
>> Note [protein kinase]
>> Aug 7, 2012 10:03:18 AM org.biojava3.genome.parsers.gff.GFF3Reader read
>> INFO: Gff.read(): Reading
>> /Users/mheuer/working/biojava-git/biojava3-genome/src/test/resources/volvox.gff3
>> Aug 7, 2012 10:03:18 AM org.biojava3.genome.parsers.gff.GFF3Reader read
>> INFO: Gff.read(): Reading
>> /Users/mheuer/working/biojava-git/biojava3-genome/src/test/resources/volvox.gff3
>> Tests run: 6, Failures: 0, Errors: 3, Skipped: 0, Time elapsed: 0.649
>> sec <<< FAILURE!
>> Running org.biojava3.genome.AppTest
>> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec
>>
>> Results :
>>
>> Tests in error:
>>   testLoadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(org.biojava3.genome.GeneFeatureHelperTest)
>>   testOutputFastaSequenceLengthGFF3(org.biojava3.genome.GeneFeatureHelperTest)
>>   testGetProteinSequences(org.biojava3.genome.GeneFeatureHelperTest)
>>
>> ...
>>
>> -------------------------------------------------------------------------------
>> Test set: org.biojava3.genome.GeneFeatureHelperTest
>> -------------------------------------------------------------------------------
>> Tests run: 6, Failures: 0, Errors: 3, Skipped: 0, Time elapsed: 0.648
>> sec <<< FAILURE!
>> testLoadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(org.biojava3.genome.GeneFeatureHelperTest)
>>  Time elapsed: 0.156 sec  <<< ERROR!
>> java.io.FileNotFoundException:
>> src/test/resources/testoutput/volvox_all_genes_exon_uppercase.gff3 (No
>> such file or directory)
>>         at java.io.FileOutputStream.open(Native Method)
>>         at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
>>         at java.io.FileOutputStream.<init>(FileOutputStream.java:84)
>>         at org.biojava3.genome.GeneFeatureHelperTest.testLoadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(GeneFeatureHelperTest.java:63)
>> ...
>> testOutputFastaSequenceLengthGFF3(org.biojava3.genome.GeneFeatureHelperTest)
>>  Time elapsed: 0.007 sec  <<< ERROR!
>> java.io.FileNotFoundException:
>> src/test/resources/testoutput/volvox_length.gff3 (No such file or
>> directory)
>>         at java.io.FileOutputStream.open(Native Method)
>>         at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
>>         at java.io.FileOutputStream.<init>(FileOutputStream.java:145)
>>         at java.io.FileWriter.<init>(FileWriter.java:73)
>>         at org.biojava3.genome.GeneFeatureHelper.outputFastaSequenceLengthGFF3(GeneFeatureHelper.java:163)
>>         at org.biojava3.genome.GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3(GeneFeatureHelperTest.java:78)
>> ...
>> testGetProteinSequences(org.biojava3.genome.GeneFeatureHelperTest)
>> Time elapsed: 0.152 sec  <<< ERROR!
>> java.io.FileNotFoundException:
>> src/test/resources/testoutput/volvox_all.faa (No such file or
>> directory)
>>         at java.io.FileOutputStream.open(Native Method)
>>         at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
>>         at java.io.FileOutputStream.<init>(FileOutputStream.java:145)
>>         at org.biojava3.core.sequence.io.FastaWriterHelper.writeProteinSequence(FastaWriterHelper.java:57)
>>         at org.biojava3.genome.GeneFeatureHelperTest.testGetProteinSequences(GeneFeatureHelperTest.java:107)
>>
>>
>> This directory is not present
>>
>> src/test/resources/testoutput
>>
>> nor is this one
>>
>> biojava3-genome/src/test/resources/testoutput
>>
>> Files that are written out during unit tests should probably use
>> File.createTempFile(...).
>>
>>
>> svn trunk built fine for me on linux last night.  ssh is blocked at
>> work so I cannot try svn trunk here.
>>
>>    michael
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