<div dir="ltr"><div><div>Yes Jose, you got it!<br></div>I modified assertBinaryEquals with assertEquals and now the test passes.<br><br></div>Good job. I can push a patch if you are of the same opinion.<br><br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-07-15 11:16 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">
I am testing on Linux and all works fine. From your output it seems
that you are in cygwin/windows, aren't you? <br>
<br>
I've had a look now into the test that fails
(GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3) and I'd
say that it must be an issue of new line character differences
between windows/unix.<br>
<br>
The test tries to compare the BioJava-produced output file to a
master file stored in the resources dir. The comparison is done with
FileAssert.assertBinaryEquals() and that must be the problem: 1 file
is written in windows and the other must be from unix, so they won't
be the same binary-wise, I suppose because of the new lines (perhaps
also the tabs?).<br>
<br>
I can't test it here properly without a Windows system, could you
see if you can fix the test? I'd suggest simply replacing the binary
comparison with a text-based comparison.<br>
<br>
Cheers<span class="HOEnZb"><font color="#888888"><br>
<br>
Jose</font></span><div><div class="h5"><br>
<br>
<br>
<div>On 15.07.2015 10:56, Paolo Pavan wrote:<br>
</div>
<blockquote type="cite">
<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" target="_blank">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><font color="#888888"><br>
<br>
Jose</font></span>
<div>
<div><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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