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

Jose Duarte jose.duarte at rcsb.org
Wed May 23 20:36:42 UTC 2018 

If what you want is to use biojava in your project, then you don't need to
clone biojava at all.

Instead you simply make your project a maven project (have a look at a
tutorial, there's plenty around) and add the latest biojava release as a
dependency with this:

    <dependencies>
      <dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-core</artifactId>
        <version>5.0.2</version>
      </dependency>
      <!-- other biojava dependencies as needed -->
    </dependencies>


Once you have the dependency you can then use biojava classes within your
project. Maven will pick everything up automatically.

Jose


On Wed, May 23, 2018 at 12:26 PM, Caitlin <bioprogrammer at gmail.com> wrote:

> 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
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>
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