[Biojava-l] Help with building BioJava using Maven?

[Caitlin]

Hi all.

I am completely inexperienced with respect to using Maven and I am
encountering immense difficulty in building the latest version that I have
cloned from GitHub.

After entering the BioJava folder, edited my pom.xml file to include the
following dependencies:

    <dependencyManagement>
<dependencies>
      <dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-core</artifactId>
        <version>5.1.0-SNAPSHOT </version>
      </dependency>

<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-aa-prop</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>

<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-alignment</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>

<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-genome</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>

<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-integrationtest</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>


<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-modfinder</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>


<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-ontology</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>



<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-protein-disorder</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>



<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-structure-gui</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>



<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-structure</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>


<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-survival</artifactId>
        <version>5.1.0-SNAPSHOT</version>
      </dependency>

<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-ws</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>

I then issued the command "mvn clean" which displayed the message "Build
Success". I then issued "mvn install" which failed with:

[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0.377 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
[ERROR] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed:
0.35 s <<< FAILURE! - in
org.biojava.nbio.core.util.TestUncompressInputStream
[ERROR]
testUncompression(org.biojava.nbio.core.util.TestUncompressInputStream)
Time elapsed: 0.31 s  <<< FAILURE!
java.lang.AssertionError: array lengths differed, expected.length=9068
actual.length=9257
        at
org.biojava.nbio.core.util.TestUncompressInputStream.testUncompression(TestUncompressInputStream.java:70)

[INFO]
[INFO] Results:
[INFO]
[ERROR] Failures:
[ERROR]   TestUncompressInputStream.testUncompression:70 array lengths
differed, expected.length=9068 actual.length=9257
[INFO]
[ERROR] Tests run: 244, Failures: 1, Errors: 0, Skipped: 6
[INFO]
[INFO]
------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] biojava-core 5.1.0-SNAPSHOT ........................ FAILURE [01:35
min]
[INFO] biojava-alignment 5.1.0-SNAPSHOT ................... SKIPPED
[INFO] biojava-structure 5.1.0-SNAPSHOT ................... SKIPPED
[INFO] biojava-structure-gui 5.1.0-SNAPSHOT ............... SKIPPED
[INFO] biojava-genome 5.1.0-SNAPSHOT ...................... SKIPPED
[INFO] biojava-modfinder 5.1.0-SNAPSHOT ................... SKIPPED
[INFO] biojava-ws 5.1.0-SNAPSHOT .......................... SKIPPED
[INFO] biojava-protein-disorder 5.1.0-SNAPSHOT ............ SKIPPED
[INFO] biojava-aa-prop 5.1.0-SNAPSHOT ..................... SKIPPED
[INFO] biojava-survival 5.1.0-SNAPSHOT .................... SKIPPED
[INFO] biojava-ontology 5.1.0-SNAPSHOT .................... SKIPPED
[INFO] biojava-integrationtest 5.1.0-SNAPSHOT ............. SKIPPED
[INFO] biojava 4.2.2 ...................................... SKIPPED
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 01:36 min
[INFO] Finished at: 2018-05-23T12:26:00-07:00
[INFO]
------------------------------------------------------------------------
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-surefire-plugin:2.21.0:test (default-test)
on project biojava-core: There are test failures.
[ERROR]
[ERROR] Please refer to
C:\Users\CaitlinG\biojava\biojava-core\target\surefire-reports for the
individual test results.
[ERROR] Please refer to dump files (if any exist) [date]-jvmRun[N].dump,
[date].dumpstream and [date]-jvmRun[N].dumpstream.
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e
switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions,
please read the following articles:
[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

C:\Users\CaitlinG\biojava>

Thank you for any help you can offer.

~Caitlin
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