<div dir="ltr">If what you want is to use biojava in your project, then you don't need to clone biojava at all. <div><br></div><div>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:</div><div><br></div><div><pre style="box-sizing:border-box;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,Courier,monospace;font-size:13.6px;margin-top:0px;margin-bottom:0px;word-wrap:normal;padding:16px;overflow:auto;line-height:1.45;background-color:rgb(246,248,250);border-radius:3px;word-break:normal;color:rgb(36,41,46);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial"> <<span class="gmail-pl-ent" style="box-sizing:border-box;color:rgb(34,134,58)">dependencies</span>>
<<span class="gmail-pl-ent" style="box-sizing:border-box;color:rgb(34,134,58)">dependency</span>>
<<span class="gmail-pl-ent" style="box-sizing:border-box;color:rgb(34,134,58)">groupId</span>>org.biojava</<span class="gmail-pl-ent" style="box-sizing:border-box;color:rgb(34,134,58)">groupId</span>>
<<span class="gmail-pl-ent" style="box-sizing:border-box;color:rgb(34,134,58)">artifactId</span>>biojava-core</<span class="gmail-pl-ent" style="box-sizing:border-box;color:rgb(34,134,58)">artifactId</span>>
<<span class="gmail-pl-ent" style="box-sizing:border-box;color:rgb(34,134,58)">version</span>>5.0.2</<span class="gmail-pl-ent" style="box-sizing:border-box;color:rgb(34,134,58)">version</span>>
</<span class="gmail-pl-ent" style="box-sizing:border-box;color:rgb(34,134,58)">dependency</span>>
<span class="gmail-pl-c" style="box-sizing:border-box;color:rgb(106,115,125)"><span class="gmail-pl-c" style="box-sizing:border-box;color:rgb(106,115,125)"><!--</span> other biojava dependencies as needed <span class="gmail-pl-c" style="box-sizing:border-box;color:rgb(106,115,125)">--></span></span>
</<span class="gmail-pl-ent" style="box-sizing:border-box;color:rgb(34,134,58)">dependencies</span>></pre><br></div><div>Once you have the dependency you can then use biojava classes within your project. Maven will pick everything up automatically.</div><div><br></div><div>Jose</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, May 23, 2018 at 12:26 PM, Caitlin <span dir="ltr"><<a href="mailto:bioprogrammer@gmail.com" target="_blank">bioprogrammer@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi all.</div><div><br></div><div>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.</div><div><br></div><div>After entering the BioJava folder, edited my pom.xml file to include the following dependencies:</div><div><br></div><div> <dependencyManagement><br><dependencies><br> <dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-core</<wbr>artifactId><br> <version>5.1.0-SNAPSHOT
</version><br> </dependency><br> <br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-aa-prop</<wbr>artifactId><br> <version>
5.1.0-SNAPSHOT
</version><br> </dependency><br><br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-alignment<<wbr>/artifactId><br> <version>
5.1.0-SNAPSHOT </version><br> </dependency><br><br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-genome</<wbr>artifactId><br> <version>
5.1.0-SNAPSHOT
</version><br> </dependency><br><br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-<wbr>integrationtest</artifactId><br> <version>
5.1.0-SNAPSHOT
</version><br> </dependency><br><br><br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-modfinder<<wbr>/artifactId><br> <version>
5.1.0-SNAPSHOT
</version><br> </dependency><br><br><br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-ontology</<wbr>artifactId><br> <version>
5.1.0-SNAPSHOT
</version><br> </dependency><br><br><br><br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-protein-<wbr>disorder</artifactId><br> <version>
5.1.0-SNAPSHOT
</version><br> </dependency><br><br><br><br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-structure-<wbr>gui</artifactId><br> <version>
5.1.0-SNAPSHOT
</version><br> </dependency><br><br><br><br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-structure<<wbr>/artifactId><br> <version>
5.1.0-SNAPSHOT
</version><br> </dependency><br><br><br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-survival</<wbr>artifactId><br> <version>5.1.0-SNAPSHOT</<wbr>version><br> </dependency><br><br><dependency><br> <groupId>org.biojava</groupId><br> <artifactId>biojava-ws</<wbr>artifactId><br> <version>
5.1.0-SNAPSHOT
</version><br> </dependency></div><div><br></div><div>I then issued the command "mvn clean" which displayed the message "Build Success". I then issued "mvn install" which failed with:</div><div><br></div><div>[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.377 s - in org.biojava.nbio.core.<wbr>TestAmbiguityCompoundSet<br>[INFO] Running org.biojava.nbio.core.util.<wbr>TestUncompressInputStream<br>[ERROR] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.35 s <<< FAILURE! - in org.biojava.nbio.core.util.<wbr>TestUncompressInputStream<br>[ERROR] testUncompression(org.biojava.<wbr>nbio.core.util.<wbr>TestUncompressInputStream) Time elapsed: 0.31 s <<< FAILURE!<br>java.lang.AssertionError: array lengths differed, expected.length=9068 actual.length=9257<br> at org.biojava.nbio.core.util.<wbr>TestUncompressInputStream.<wbr>testUncompression(<wbr>TestUncompressInputStream.<wbr>java:70)<br><br>[INFO]<br>[INFO] Results:<br>[INFO]<br>[ERROR] Failures:<br>[ERROR] TestUncompressInputStream.<wbr>testUncompression:70 array lengths differed, expected.length=9068 actual.length=9257<br>[INFO]<br>[ERROR] Tests run: 244, Failures: 1, Errors: 0, Skipped: 6<br>[INFO]<br>[INFO] ------------------------------<wbr>------------------------------<wbr>------------<br>[INFO] Reactor Summary:<br>[INFO]<br>[INFO] biojava-core 5.1.0-SNAPSHOT ........................ FAILURE [01:35 min]<br>[INFO] biojava-alignment 5.1.0-SNAPSHOT ................... SKIPPED<br>[INFO] biojava-structure 5.1.0-SNAPSHOT ................... SKIPPED<br>[INFO] biojava-structure-gui 5.1.0-SNAPSHOT ............... SKIPPED<br>[INFO] biojava-genome 5.1.0-SNAPSHOT ...................... SKIPPED<br>[INFO] biojava-modfinder 5.1.0-SNAPSHOT ................... SKIPPED<br>[INFO] biojava-ws 5.1.0-SNAPSHOT .......................... SKIPPED<br>[INFO] biojava-protein-disorder 5.1.0-SNAPSHOT ............ SKIPPED<br>[INFO] biojava-aa-prop 5.1.0-SNAPSHOT ..................... SKIPPED<br>[INFO] biojava-survival 5.1.0-SNAPSHOT .................... SKIPPED<br>[INFO] biojava-ontology 5.1.0-SNAPSHOT .................... SKIPPED<br>[INFO] biojava-integrationtest 5.1.0-SNAPSHOT ............. SKIPPED<br>[INFO] biojava 4.2.2 ..............................<wbr>........ SKIPPED<br>[INFO] ------------------------------<wbr>------------------------------<wbr>------------<br>[INFO] BUILD FAILURE<br>[INFO] ------------------------------<wbr>------------------------------<wbr>------------<br>[INFO] Total time: 01:36 min<br>[INFO] Finished at: 2018-05-23T12:26:00-07:00<br>[INFO] ------------------------------<wbr>------------------------------<wbr>------------<br>[ERROR] Failed to execute goal org.apache.maven.plugins:<wbr>maven-surefire-plugin:2.21.0:<wbr>test (default-test) on project biojava-core: There are test failures.<br>[ERROR]<br>[ERROR] Please refer to C:\Users\CaitlinG\biojava\<wbr>biojava-core\target\surefire-<wbr>reports for the individual test results.<br>[ERROR] Please refer to dump files (if any exist) [date]-jvmRun[N].dump, [date].dumpstream and [date]-jvmRun[N].dumpstream.<br>[ERROR] -> [Help 1]<br>[ERROR]<br>[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.<br>[ERROR] Re-run Maven using the -X switch to enable full debug logging.<br>[ERROR]<br>[ERROR] For more information about the errors and possible solutions, please read the following articles:<br>[ERROR] [Help 1] <a href="http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException" target="_blank">http://cwiki.apache.org/<wbr>confluence/display/MAVEN/<wbr>MojoFailureException</a><br><br>C:\Users\CaitlinG\biojava></div><div><br></div><div>Thank you for any help you can offer.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>~Caitlin</div><div><br></div><div><br></div><div><br></div></font></span></div>
<br>______________________________<wbr>_________________<br>
Biojava-l mailing list - <a href="mailto:Biojava-l@mailman.open-bio.org">Biojava-l@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-l" rel="noreferrer" target="_blank">http://mailman.open-bio.org/<wbr>mailman/listinfo/biojava-l</a><br></blockquote></div><br></div>