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linikujp / owltools

Automatically exported from code.google.com/p/owltools
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Trouble building OortCommandLine #103

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. svn checkout http://owltools.googlecode.com/svn/trunk/ owltools-read-only
2. cd ./owltools-read-only/OWLTools-Parent
3. mvn clean package

The expected output is a successful build of Oort Command Line Tools. Instead, 
errors are reported and the result is not a functioning build. An excerpt of 
maven's output that includes error messages is included below.

The error occurs with a fresh copy of http://owltools.googlecode.com/svn/trunk/ 
obtained on Friday, September 26 2014 by following step (1) above. The versions 
of Maven, Java, and Linux used are as follows:

$ mvn -V
Apache Maven 3.0.4
Maven home: /usr/share/maven
Java version: 1.7.0_65, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-7-openjdk-i386/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "3.2.0-68-generic", arch: "i386", family: "unix"

I experienced a similar issue last week trying to build on Mac OS 10.9.5

---Maven excerpt-----

### Annotations:

 * [comment](http://www.w3.org/2000/01/rdf-schema#comment) : 
          foo

 * [creator](http://purl.org/dc/elements/1.1/creator) : Gene Ontology Consortium
 * [homepage](http://xmlns.com/foaf/0.1/homepage) : [http://wiki.geneontology.org/index.php/Ontology_extensions](http://wiki.geneontology.org/index.php/Ontology_extensions)
 * [publisher](http://purl.org/dc/elements/1.1/publisher) : Gene Ontology Consortium

Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec

Results :

Tests in error: 
  testConvertXPs(owltools.CycleTest): Unexpected end of file from server

Tests run: 144, Failures: 0, Errors: 1, Skipped: 3

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] OWLTools-Parent ................................... SUCCESS [43.531s]
[INFO] OWLTools-Core ..................................... FAILURE [13:42.922s]
[INFO] Lego .............................................. SKIPPED
[INFO] OWLTools-Annotation ............................... SKIPPED
[INFO] OWLTools-Oort ..................................... SKIPPED
[INFO] OWLTools-Sim ...................................... SKIPPED
[INFO] OWLTools-Web ...................................... SKIPPED
[INFO] OWLTools-Solr ..................................... SKIPPED
[INFO] OWLTools-Runner ................................... SKIPPED
[INFO] OWLTools-NCBI ..................................... SKIPPED
[INFO] MolecularModelServer .............................. SKIPPED
[INFO] Golr-Client ....................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 14:26.784s
[INFO] Finished at: Fri Sep 26 11:08:26 EDT 2014
[INFO] Final Memory: 20M/69M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal 
org.apache.maven.plugins:maven-surefire-plugin:2.12.2:test (default-test) on 
project OWLTools-Core: There are test failures.
[ERROR] 
[ERROR] Please refer to 
/home/jonathanbona/Desktop/owltools-read-only/OWLTools-Core/target/surefire-repo
rts for the individual test results.
[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
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :OWLTools-Core

Original issue reported on code.google.com by jonathan...@gmail.com on 26 Sep 2014 at 3:30

GoogleCodeExporter commented 9 years ago 
Hello,
thank you for reporting the issue. The problem with this particular test is 
that it tries to load an ontology via an HTTP request. This may fail for 
numerous reasons.

To prevent further false positive, I have added an ignore tag to this test.

In general, we have a continuous integration test running here: 
http://build.berkeleybop.org/job/owltools/
As long as this jobs runs though okay, we assume the owltools build is okay.

Original comment by HDie...@lbl.gov on 26 Sep 2014 at 5:05

GoogleCodeExporter commented 9 years ago 
Thanks!

Original comment by jonathan...@gmail.com on 26 Sep 2014 at 7:31