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    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<br>
    <br>
    Jose<br>
    <br>
    <br>
    <div class="moz-cite-prefix">On 15.07.2015 10:56, Paolo Pavan wrote:<br>
    </div>
    <blockquote
cite="mid:CAD2LbkyFBJ+Jb_6wJE+gT=SX-nhJJ+QMUEQr+-+Db_s6-PtP_Q@mail.gmail.com"
      type="cite">
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          <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
        &lt;argLine&gt;-Dfile.encoding=...&lt;argLine&gt; 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 &lt;&lt;&lt; FAILURE! - in
        org.biojava.nbio.genome.GeneFeatureHelperTest<br>
        testOutputFastaSequenceLengthGFF3(org.biojava.nbio.genome.GeneFeatureHelperTest) 
        Time elapsed: 0.198 sec  &lt;&lt;&lt; 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>
        -&gt; [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 moz-do-not-send="true"
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">&lt;<a moz-do-not-send="true"
              href="mailto:jose.duarte@psi.ch" target="_blank">jose.duarte@psi.ch</a>&gt;</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 &lt;&lt;&lt;
                          FAILURE! - in
                          org.biojava.nbio.genome.GeneFeatureHelperTest<br>
                          testOutputFastaSequenceLengthGFF3(org.biojava.nbio.genome.GeneFeatureHelperTest) 

                          Time elapsed: 0.199 sec  &lt;&lt;&lt; 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">&lt;<a
                            moz-do-not-send="true"
                            href="mailto:jose.duarte@psi.ch"
                            target="_blank">jose.duarte@psi.ch</a>&gt;</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>
                              <pre>_______________________________________________
biojava-dev mailing list
<a moz-do-not-send="true" href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a>
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                            </blockquote>
                            <br>
                          </div>
                          <br>
_______________________________________________<br>
                          biojava-dev mailing list<br>
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                            href="mailto:biojava-dev@mailman.open-bio.org"
                            target="_blank">biojava-dev@mailman.open-bio.org</a><br>
                          <a moz-do-not-send="true"
                            href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev"
                            rel="noreferrer" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
                        </blockquote>
                      </div>
                      <br>
                    </div>
                  </blockquote>
                  <br>
                </div>
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          </blockquote>
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