Help with building BioJava using Maven?
Caitlin <[email protected]> Wed, 23 May 2018 12:26:39 -0700
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CABDKo+wpwU3hasDokm1sCuvXKwfJ8EQnze=bpnM2=i9=T-uz-g@mail.gmail.com> |
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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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<div dir=3D"ltr"><div>Hi all.</div><div><br></div><div>I am completely inex=
perienced with respect to using Maven and I am encountering immense difficu=
lty in building the latest version that I have cloned from GitHub.</div><di=
v><br></div><div>After entering the BioJava folder, edited my pom.xml file =
to include the following dependencies:</div><div><br></div><div>=C2=A0=C2=
=A0=C2=A0 <dependencyManagement><br><dependencies><br>=C2=A0=C2=
=A0=C2=A0=C2=A0=C2=A0 <dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0 <groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0 <artifactId>biojava-core</artifactId&g=
t;<br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>5.1.0-SNAPS=
HOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br>=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <br><dependency><br>=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0=C2=A0=C2=A0 <groupId>org.biojava</groupId><br>=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <artifactId>biojava-aa-prop&l=
t;/artifactId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version=
>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <gro=
upId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0 <artifactId>biojava-alignment</artifactId><br>=C2=A0=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT </version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </depe=
ndency><br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0 <groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0=C2=A0=C2=A0 <artifactId>biojava-genome</artifactId>=
;<br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <gro=
upId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0 <artifactId>biojava-integrationtest</artifactId><br>=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <=
;groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0 <artifactId>biojava-modfinder</artifactId><br>=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <=
;groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0 <artifactId>biojava-ontology</artifactId><br>=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
<groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0 <artifactId>biojava-protein-disorder</artifactId&g=
t;<br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
<groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0 <artifactId>biojava-structure-gui</artifactId><=
br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
<groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0 <artifactId>biojava-structure</artifactId><br>=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <=
;groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0 <artifactId>biojava-survival</artifactId><br>=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>5.1.0-SNAPSHOT</v=
ersion><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><br><=
;dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <groupId&g=
t;org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
<artifactId>biojava-ws</artifactId><br>=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency></div=
><div><br></div><div>I then issued the command "mvn clean" which =
displayed the message "Build Success". I then issued "mvn in=
stall" 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.biojav=
a.nbio.core.TestAmbiguityCompoundSet<br>[INFO] Running org.biojava.nbio.cor=
e.util.TestUncompressInputStream<br>[ERROR] Tests run: 1, Failures: 1, Erro=
rs: 0, Skipped: 0, Time elapsed: 0.35 s <<< FAILURE! - in org.bioj=
ava.nbio.core.util.TestUncompressInputStream<br>[ERROR] testUncompression(o=
rg.biojava.nbio.core.util.TestUncompressInputStream)=C2=A0 Time elapsed: 0.=
31 s=C2=A0 <<< FAILURE!<br>java.lang.AssertionError: array lengths=
differed, expected.length=3D9068 actual.length=3D9257<br>=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0 at org.biojava.nbio.core.util.TestUncompressInp=
utStream.testUncompression(TestUncompressInputStream.java:70)<br><br>[INFO]=
<br>[INFO] Results:<br>[INFO]<br>[ERROR] Failures:<br>[ERROR]=C2=A0=C2=A0 T=
estUncompressInputStream.testUncompression:70 array lengths differed, expec=
ted.length=3D9068 actual.length=3D9257<br>[INFO]<br>[ERROR] Tests run: 244,=
Failures: 1, Errors: 0, Skipped: 6<br>[INFO]<br>[INFO] -------------------=
-----------------------------------------------------<br>[INFO] Reactor Sum=
mary:<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 ................... SKIP=
PED<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] bi=
ojava-ontology 5.1.0-SNAPSHOT .................... SKIPPED<br>[INFO] biojav=
a-integrationtest 5.1.0-SNAPSHOT ............. SKIPPED<br>[INFO] biojava 4.=
2.2 ...................................... SKIPPED<br>[INFO] --------------=
----------------------------------------------------------<br>[INFO] BUILD =
FAILURE<br>[INFO] ---------------------------------------------------------=
---------------<br>[INFO] Total time: 01:36 min<br>[INFO] Finished at: 2018=
-05-23T12:26:00-07:00<br>[INFO] -------------------------------------------=
-----------------------------<br>[ERROR] Failed to execute goal org.apache.=
maven.plugins:maven-surefire-plugin:2.21.0:test (default-test) on project b=
iojava-core: There are test failures.<br>[ERROR]<br>[ERROR] Please refer to=
C:\Users\CaitlinG\biojava\biojava-core\target\surefire-reports for the ind=
ividual test results.<br>[ERROR] Please refer to dump files (if any exist) =
[date]-jvmRun[N].dump, [date].dumpstream and [date]-jvmRun[N].dumpstream.<b=
r>[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 usi=
ng the -X switch to enable full debug logging.<br>[ERROR]<br>[ERROR] For mo=
re information about the errors and possible solutions, please read the fol=
lowing articles:<br>[ERROR] [Help 1] <a href=3D"http://cwiki.apache.org/con=
fluence/display/MAVEN/MojoFailureException">http://cwiki.apache.org/conflue=
nce/display/MAVEN/MojoFailureException</a><br><br>C:\Users\CaitlinG\biojava=
></div><div><br></div><div>Thank you for any help you can offer.</div><d=
iv><br></div><div>~Caitlin</div><div><br></div><div><br></div><div><br></di=
v></div>
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