[Biojava-dev] Biojava genome test fails
Paolo Pavan
paolo.pavan at gmail.com
Wed Jul 15 08:56:13 UTC 2015
Hi Jose,
I tried it without success:
CLEAN:
$ /cygdrive/c/Program\ Files/NetBeans\ 8.0.2/java/maven/bin/mvn clean
[INFO] Scanning for projects...
[INFO] Inspecting build with total of 1 modules...
[INFO] Installing Nexus Staging features:
[INFO] ... total of 1 executions of maven-deploy-plugin replaced with
nexus-staging-maven-plugin
[INFO]
[INFO]
------------------------------------------------------------------------
[INFO] Building biojava-genome 4.1.1-SNAPSHOT
[INFO]
------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.6.1:clean (default-clean) @ biojava-genome
---
[INFO] Deleting
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\target
[INFO]
------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 1.038s
[INFO] Finished at: Wed Jul 15 10:46:47 CEST 2015
[INFO] Final Memory: 9M/232M
[INFO]
------------------------------------------------------------------------
TEST:
cd C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome;
"JAVA_HOME=C:\\Program Files\\Java\\jdk1.8.0_45" cmd /c "\"\"C:\\Program
Files\\NetBeans 8.0.2\\java\\maven\\bin\\mvn.bat\"
-Dmaven.ext.class.path=\"C:\\Program Files\\NetBeans
8.0.2\\java\\maven-nblib\\netbeans-eventspy.jar\" -Dfile.encoding=UTF-8
install\""
Scanning for projects...
Inspecting build with total of 1 modules...
Installing Nexus Staging features:
... total of 1 executions of maven-deploy-plugin replaced with
nexus-staging-maven-plugin
------------------------------------------------------------------------
Building biojava-genome 4.1.1-SNAPSHOT
------------------------------------------------------------------------
--- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ biojava-genome ---
--- maven-resources-plugin:2.5:resources (default-resources) @
biojava-genome ---
[debug] execute contextualize
Using 'UTF-8' encoding to copy filtered resources.
Copying 1 resource
--- maven-compiler-plugin:3.3:compile (default-compile) @ biojava-genome ---
Changes detected - recompiling the module!
Compiling 28 source files to
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\target\classes
--- maven-resources-plugin:2.5:testResources (default-testResources) @
biojava-genome ---
[debug] execute contextualize
Using 'UTF-8' encoding to copy filtered resources.
Copying 9 resources
--- maven-compiler-plugin:3.3:testCompile (default-testCompile) @
biojava-genome ---
Changes detected - recompiling the module!
Compiling 3 source files to
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\target\test-classes
--- maven-surefire-plugin:2.18.1:test (default-test) @ biojava-genome ---
Surefire report directory:
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\target\surefire-reports
file.encoding cannot be set as system property, use
<argLine>-Dfile.encoding=...<argLine> instead
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.biojava.nbio.genome.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec -
in org.biojava.nbio.genome.AppTest
Running org.biojava.nbio.genome.FeatureListTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.429 sec -
in org.biojava.nbio.genome.FeatureListTest
Running org.biojava.nbio.genome.GeneFeatureHelperTest
10:47:18 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader -
Reading:
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
10:47:18 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader -
Reading: src/test/resources/amphimedon.gff3
10:47:18 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader -
Reading:
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
10:47:19 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader -
Reading:
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
10:47:19 [main] INFO org.biojava.nbio.genome.GeneFeatureHelperTest - Note
[protein kinase]
10:47:19 [main] INFO org.biojava.nbio.genome.GeneFeatureHelper - Gene EDEN
found at ctgA 1050 9000 POSITIVE
10:47:19 [main] INFO org.biojava.nbio.genome.GeneFeatureHelper - Gene
rna-Apple3 found at ctgA 18000 21200 POSITIVE
Tests run: 6, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.592 sec
<<< FAILURE! - in org.biojava.nbio.genome.GeneFeatureHelperTest
testOutputFastaSequenceLengthGFF3(org.biojava.nbio.genome.GeneFeatureHelperTest)
Time elapsed: 0.198 sec <<< FAILURE!
junit.framework.AssertionFailedError: actual file is shorter
at junit.framework.Assert.fail(Assert.java:57)
at junitx.framework.FileAssert.assertBinaryEquals(FileAssert.java:240)
at
org.biojava.nbio.genome.GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3(GeneFeatureHelperTest.java:105)
Results :
Failed tests:
GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3:105 actual file
is shorter
Tests run: 8, Failures: 1, Errors: 0, Skipped: 0
------------------------------------------------------------------------
BUILD FAILURE
------------------------------------------------------------------------
Total time: 7.597s
Finished at: Wed Jul 15 10:47:19 CEST 2015
Final Memory: 22M/403M
------------------------------------------------------------------------
Failed to execute goal
org.apache.maven.plugins:maven-surefire-plugin:2.18.1:test (default-test)
on project biojava-genome: There are test failures.
Please refer to
C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\target\surefire-reports
for the individual test results.
-> [Help 1]
To see the full stack trace of the errors, re-run Maven with the -e switch.
Re-run Maven using the -X switch to enable full debug logging.
For more information about the errors and possible solutions, please read
the following articles:
[Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
2015-07-14 19:55 GMT+02:00 Jose Manuel Duarte <jose.duarte at psi.ch>:
> Maybe some files left over from a broken run? Try see if cleaning (mvn
> clean) and then building again does the trick.
>
> Jose
>
>
>
> On 14.07.2015 18:11, Paolo Pavan wrote:
>
> Hi Jose,
> Interesting! I'm also working on commit
> 154edb7f9a5e9e54f25df3e27aeb169b4fab7799 and below is the result. At a
> first glance it does not seem a network problem, it downloads
> maven-metadata.xml.
> What do you think?
> Paolo
>
> -------------------------------------------------------
> T E S T S
> -------------------------------------------------------
> Running org.biojava.nbio.genome.AppTest
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec
> - in org.biojava.nbio.genome.AppTest
> Running org.biojava.nbio.genome.FeatureListTest
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.502 sec
> - in org.biojava.nbio.genome.FeatureListTest
> Running org.biojava.nbio.genome.GeneFeatureHelperTest
> 18:04:40 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader -
> Reading:
> C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
> 18:04:41 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader -
> Reading: src/test/resources/amphimedon.gff3
> 18:04:41 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader -
> Reading:
> C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
> 18:04:41 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader -
> Reading:
> C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
> 18:04:41 [main] INFO org.biojava.nbio.genome.GeneFeatureHelperTest - Note
> [protein kinase]
> 18:04:41 [main] INFO org.biojava.nbio.genome.GeneFeatureHelper - Gene
> EDEN found at ctgA 1050 9000 POSITIVE
> 18:04:41 [main] INFO org.biojava.nbio.genome.GeneFeatureHelper - Gene
> rna-Apple3 found at ctgA 18000 21200 POSITIVE
> Tests run: 6, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.598 sec
> <<< FAILURE! - in org.biojava.nbio.genome.GeneFeatureHelperTest
> testOutputFastaSequenceLengthGFF3(org.biojava.nbio.genome.GeneFeatureHelperTest)
> Time elapsed: 0.199 sec <<< FAILURE!
> junit.framework.AssertionFailedError: actual file is shorter
> at junit.framework.Assert.fail(Assert.java:57)
> at junitx.framework.FileAssert.assertBinaryEquals(FileAssert.java:240)
> at
> org.biojava.nbio.genome.GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3(GeneFeatureHelperTest.java:105)
>
>
> 2015-07-14 14:44 GMT+02:00 Jose Manuel Duarte <jose.duarte at psi.ch>:
>
>> It works for me (on commit 154edb7f9a5e9e).
>>
>> Could that be some kind of network problem?
>>
>> Jose
>>
>>
>>
>> On 14.07.2015 14:32, Paolo Pavan wrote:
>>
>> Hello,
>> It seems that testOutputFastaSequenceLengthGFF3 fails in biojava-genome
>> 4.1.1 snapshot.
>> Is this happening to someone else?
>>
>> bye bye,
>> Paolo
>>
>>
>> _______________________________________________
>> biojava-dev mailing listbiojava-dev at mailman.open-bio.orghttp://mailman.open-bio.org/mailman/listinfo/biojava-dev
>>
>>
>>
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>> biojava-dev mailing list
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>>
>
>
>
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