<div dir="ltr"><div><div>Hi Jose,<br></div>I tried it without success:<br><br><br>CLEAN:<br>$ /cygdrive/c/Program\ Files/NetBeans\ 8.0.2/java/maven/bin/mvn clean<br>[INFO] Scanning for projects...<br>[INFO] Inspecting build with total of 1 modules...<br>[INFO] Installing Nexus Staging features:<br>[INFO] ... total of 1 executions of maven-deploy-plugin replaced with nexus-staging-maven-plugin<br>[INFO]<br>[INFO] ------------------------------------------------------------------------<br>[INFO] Building biojava-genome 4.1.1-SNAPSHOT<br>[INFO] ------------------------------------------------------------------------<br>[INFO]<br>[INFO] --- maven-clean-plugin:2.6.1:clean (default-clean) @ biojava-genome ---<br>[INFO] Deleting C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\target<br>[INFO] ------------------------------------------------------------------------<br>[INFO] BUILD SUCCESS<br>[INFO] ------------------------------------------------------------------------<br>[INFO] Total time: 1.038s<br>[INFO] Finished at: Wed Jul 15 10:46:47 CEST 2015<br>[INFO] Final Memory: 9M/232M<br>[INFO] ------------------------------------------------------------------------<br><br></div>TEST:<br><br>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\""<br>Scanning for projects...<br>Inspecting build with total of 1 modules...<br>Installing Nexus Staging features:<br> ... total of 1 executions of maven-deploy-plugin replaced with nexus-staging-maven-plugin<br> <br>------------------------------------------------------------------------<br>Building biojava-genome 4.1.1-SNAPSHOT<br>------------------------------------------------------------------------<br><br>--- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ biojava-genome ---<br><br>--- maven-resources-plugin:2.5:resources (default-resources) @ biojava-genome ---<br>[debug] execute contextualize<br>Using 'UTF-8' encoding to copy filtered resources.<br>Copying 1 resource<br><br>--- maven-compiler-plugin:3.3:compile (default-compile) @ biojava-genome ---<br>Changes detected - recompiling the module!<br>Compiling 28 source files to C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\target\classes<br><br>--- maven-resources-plugin:2.5:testResources (default-testResources) @ biojava-genome ---<br>[debug] execute contextualize<br>Using 'UTF-8' encoding to copy filtered resources.<br>Copying 9 resources<br><br>--- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ biojava-genome ---<br>Changes detected - recompiling the module!<br>Compiling 3 source files to C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\target\test-classes<br><br>--- maven-surefire-plugin:2.18.1:test (default-test) @ biojava-genome ---<br>Surefire report directory: C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\target\surefire-reports<br>file.encoding cannot be set as system property, use <argLine>-Dfile.encoding=...<argLine> instead<br><br>-------------------------------------------------------<br> T E S T S<br>-------------------------------------------------------<br>Running org.biojava.nbio.genome.AppTest<br>Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec - in org.biojava.nbio.genome.AppTest<br>Running org.biojava.nbio.genome.FeatureListTest<br>Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.429 sec - in org.biojava.nbio.genome.FeatureListTest<br>Running org.biojava.nbio.genome.GeneFeatureHelperTest<br>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<br>10:47:18 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader - Reading: src/test/resources/amphimedon.gff3<br>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<br>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<br>10:47:19 [main] INFO org.biojava.nbio.genome.GeneFeatureHelperTest - Note [protein kinase]<br>10:47:19 [main] INFO org.biojava.nbio.genome.GeneFeatureHelper - Gene EDEN found at ctgA 1050 9000 POSITIVE<br>10:47:19 [main] INFO org.biojava.nbio.genome.GeneFeatureHelper - Gene rna-Apple3 found at ctgA 18000 21200 POSITIVE<br>Tests run: 6, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.592 sec <<< FAILURE! - in org.biojava.nbio.genome.GeneFeatureHelperTest<br>testOutputFastaSequenceLengthGFF3(org.biojava.nbio.genome.GeneFeatureHelperTest) Time elapsed: 0.198 sec <<< FAILURE!<br>junit.framework.AssertionFailedError: actual file is shorter<br> at junit.framework.Assert.fail(Assert.java:57)<br> at junitx.framework.FileAssert.assertBinaryEquals(FileAssert.java:240)<br> at org.biojava.nbio.genome.GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3(GeneFeatureHelperTest.java:105)<br><br><br>Results :<br><br>Failed tests: <br> GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3:105 actual file is shorter<br><br>Tests run: 8, Failures: 1, Errors: 0, Skipped: 0<br><br>------------------------------------------------------------------------<br>BUILD FAILURE<br>------------------------------------------------------------------------<br>Total time: 7.597s<br>Finished at: Wed Jul 15 10:47:19 CEST 2015<br>Final Memory: 22M/403M<br>------------------------------------------------------------------------<br>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.<br><br>Please refer to C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\target\surefire-reports for the individual test results.<br>-> [Help 1]<br><br>To see the full stack trace of the errors, re-run Maven with the -e switch.<br>Re-run Maven using the -X switch to enable full debug logging.<br><br>For more information about the errors and possible solutions, please read the following articles:<br>[Help 1] <a href="http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException">http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException</a><br><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2015-07-14 19:55 GMT+02:00 Jose Manuel Duarte <span dir="ltr"><<a href="mailto:jose.duarte@psi.ch" target="_blank">jose.duarte@psi.ch</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Maybe some files left over from a broken run? Try see if cleaning
(mvn clean) and then building again does the trick.<span class="HOEnZb"><font color="#888888"><br>
<br>
Jose</font></span><div><div class="h5"><br>
<br>
<br>
<div>On 14.07.2015 18:11, Paolo Pavan wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>Hi Jose,<br>
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. <br>
</div>
What do you think?<br>
</div>
Paolo<br>
<div>
<div><br>
-------------------------------------------------------<br>
T E S T S<br>
-------------------------------------------------------<br>
Running org.biojava.nbio.genome.AppTest<br>
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time
elapsed: 0.001 sec - in org.biojava.nbio.genome.AppTest<br>
Running org.biojava.nbio.genome.FeatureListTest<br>
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time
elapsed: 0.502 sec - in
org.biojava.nbio.genome.FeatureListTest<br>
Running org.biojava.nbio.genome.GeneFeatureHelperTest<br>
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<br>
18:04:41 [main] INFO
org.biojava.nbio.genome.parsers.gff.GFF3Reader - Reading:
src/test/resources/amphimedon.gff3<br>
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<br>
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<br>
18:04:41 [main] INFO
org.biojava.nbio.genome.GeneFeatureHelperTest - Note
[protein kinase]<br>
18:04:41 [main] INFO
org.biojava.nbio.genome.GeneFeatureHelper - Gene EDEN found
at ctgA 1050 9000 POSITIVE<br>
18:04:41 [main] INFO
org.biojava.nbio.genome.GeneFeatureHelper - Gene rna-Apple3
found at ctgA 18000 21200 POSITIVE<br>
Tests run: 6, Failures: 1, Errors: 0, Skipped: 0, Time
elapsed: 0.598 sec <<< FAILURE! - in
org.biojava.nbio.genome.GeneFeatureHelperTest<br>
testOutputFastaSequenceLengthGFF3(org.biojava.nbio.genome.GeneFeatureHelperTest)
Time elapsed: 0.199 sec <<< FAILURE!<br>
junit.framework.AssertionFailedError: actual file is shorter<br>
at junit.framework.Assert.fail(Assert.java:57)<br>
at
junitx.framework.FileAssert.assertBinaryEquals(FileAssert.java:240)<br>
at
org.biojava.nbio.genome.GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3(GeneFeatureHelperTest.java:105)<br>
<br>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2015-07-14 14:44 GMT+02:00 Jose Manuel
Duarte <span dir="ltr"><<a href="mailto:jose.duarte@psi.ch" target="_blank">jose.duarte@psi.ch</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> It works for me (on
commit 154edb7f9a5e9e).<br>
<br>
Could that be some kind of network problem?<br>
<br>
Jose
<div>
<div><br>
<br>
<br>
<div>On 14.07.2015 14:32, Paolo Pavan wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div dir="ltr">
<div>
<div>
<div>
<div>Hello,<br>
</div>
It seems that
testOutputFastaSequenceLengthGFF3 fails in
biojava-genome 4.1.1 snapshot.<br>
</div>
Is this happening to someone else?<br>
<br>
</div>
bye bye,<br>
</div>
Paolo<br>
</div>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
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