[Biojava-dev] build errors
Andreas Prlic
andreas at sdsc.edu
Fri Jan 10 01:34:44 UTC 2014
Ok, I fixed the bad URL- problems in -legacy and also exchanged the "\n"
with System.getProperty("line.separator"); in biojava 3. Both projects
compile fine for me now.
We actually do have automated builds for both -legacy and biojava 3 however
they are still behind a firewall and they kick in only if there is a commit
to a project. There was no commit to -legacy in a while so it did not pick
up on the broken URLs.
I'll talk to our sysadmin if we can get a VM to publicly host the automated
builds...
Note, besides these automated builds, there is also the (only
partially-reliable) Travis build system that is providing green or red
icons depending on the build status. (see the Build status section on
https://github.com/biojava/biojava ).
Andreas
On Wed, Jan 8, 2014 at 10:19 PM, Michael Heuer <heuermh at gmail.com> wrote:
> Hello George,
>
> I can confirm that biojava-legacy from git fails its build.
>
> $ mvn clean install
> ...
> Running org.biojava.dasobert.TestSisyphusServer
> Jan 09, 2014 12:14:48 AM org.biojava.dasobert.das.AlignmentThread
> retrieveAlignments
> INFO: requesting alignment
>
> http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/das/alignments/alignment?query%3DAL10057468
> java.io.FileNotFoundException:
>
> http://www.spice-3d.org/sisyphussisyphus/das/alignments/alignment?query%3DAL10057468
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
> at
> sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1675)
> at
> sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1673)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1671)
> at
> sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1244)
> at
> org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:188)
> at
> org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:136)
> at
> org.biojava.dasobert.das.AlignmentThread.retrieveAlignments(AlignmentThread.java:370)
> at
> org.biojava.dasobert.das.AlignmentThread.getAlignments(AlignmentThread.java:337)
> at
> org.biojava.dasobert.das.AlignmentThread.run(AlignmentThread.java:174)
> at
> org.biojava.dasobert.TestSisyphusServer.testServer(TestSisyphusServer.java:78)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at junit.framework.TestCase.runTest(TestCase.java:168)
> at junit.framework.TestCase.runBare(TestCase.java:134)
> at junit.framework.TestResult$1.protect(TestResult.java:110)
> at junit.framework.TestResult.runProtected(TestResult.java:128)
> at junit.framework.TestResult.run(TestResult.java:113)
> at junit.framework.TestCase.run(TestCase.java:124)
> at junit.framework.TestSuite.runTest(TestSuite.java:232)
> at junit.framework.TestSuite.run(TestSuite.java:227)
> at
> org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)
> at
> org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:264)
> at
> org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:153)
> at
> org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:124)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at
> org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray2(ReflectionUtils.java:208)
> at
> org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:159)
> at
> org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:87)
> at
> org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:153)
> at
> org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:95)
> Caused by: java.io.FileNotFoundException:
>
> http://www.spice-3d.org/sisyphussisyphus/das/alignments/alignment?query%3DAL10057468
> at
> sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1624)
> at
> java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468)
> at
> org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:163)
> ... 30 more
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.948 sec
> Running org.biojava.dasobert.TestSourcesParse
> unsupported capability: das1:dna
> Das2SourceHandler: source size: 267
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec
> Running org.biojava.dasobert.TestUCSCFeatures
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec
>
> Results :
>
> Tests in error:
> TestExternalSource.testExternalSource:51 » FileNotFound
> http://vega.sanger.ac....
>
> Tests run: 10, Failures: 0, Errors: 1, Skipped: 0
>
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Reactor Summary:
> [INFO]
> [INFO] biojava-legacy .................................... SUCCESS [2.177s]
> [INFO] bytecode .......................................... SUCCESS [3.124s]
> [INFO] core .............................................. SUCCESS
> [19.189s]
> [INFO] alignment ......................................... SUCCESS [0.967s]
> [INFO] biosql ............................................ SUCCESS [0.690s]
> [INFO] blast ............................................. SUCCESS [9.425s]
> [INFO] das ............................................... FAILURE
> [11.139s]
> [INFO] sequencing ........................................ SKIPPED
> [INFO] gui ............................................... SKIPPED
> [INFO] phylo ............................................. SKIPPED
> [INFO]
> ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Total time: 47.249s
> [INFO] Finished at: Thu Jan 09 00:14:50 CST 2014
> [INFO] Final Memory: 27M/373M
> [INFO]
> ------------------------------------------------------------------------
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-surefire-plugin:2.14.1:test
> (default-test) on project das: There are test failures.
>
> Might you be able to create issues for the errors you found?
>
> Thanks,
>
> michael
>
>
> On Thu, Jan 9, 2014 at 12:08 AM, George Waldon <gwaldon at geneinfinity.org>
> wrote:
> > Hi Andreas,
> >
> > No, I build the two projects separately; both are giving errors. The
> builds
> > were done using JKD1.7 (windows7/NB IDE 7.4). I do not think we still
> have
> > automatic builds for legacy; org.biojava.dasobert.TestExternalSource
> should
> > be easily reproducible. I was thinking of an end-of-line issue for the
> > others errors since
> > org.biojava3.ronn.ModelLoader.loadModels(ModelLoader.java:170) is just
> after
> > "scan.useDelimiter("\n");" suggesting my end-of-lines might have changed
> > during the checkout. No clue indeed.
> >
> > Thanks,
> > George
> >
> >
> > Quoting Andreas Prlic <andreas at sdsc.edu>:
> >
> >> Hi George,
> >>
> >> looking at your errors it seems you have a mix of biojava-legacy and
> >> biojava 3 somehow. How did you check this out? I believe the old SVN
> repo
> >> is still accessible as read only, and that is the only way I can imagine
> >> you might have gotten both.
> >>
> >> Checking out from git should be straightforward:
> >>
> >> git clone git at github.com:biojava/biojava.git ./biojava
> >>
> >> You could also try using the github application.
> >>
> >> see also: http://biojava.org/wiki/Get_source
> >>
> >> Let us know if you have any problems with that!
> >>
> >> Andreas
> >>
> >>
> >> On Mon, Jan 6, 2014 at 9:22 PM, George Waldon
> >> <gwaldon at geneinfinity.org>wrote:
> >>
> >>> Hi,
> >>>
> >>> I just started playing with git and I am getting the following build
> >>> errors, possibly an end-of-line issue somewhere but not really sure.
> >>> Could
> >>> someone help me setting git possibly?
> >>>
> >>> org.biojava.bio.seq.db.EmblCDROMIndexStoreTest
> >>> org.biojava.bio.BioException: Couldn't grab region of file
> >>> at org.biojava.bio.seq.io.FastaFormat.readSequence(
> >>> FastaFormat.java:134)
> >>> at org.biojava.bio.seq.db.IndexedSequenceDB.getSequence(
> >>> IndexedSequenceDB.java:267)
> >>> at org.biojava.bio.seq.db.EmblCDROMIndexStoreTest.testFetch(
> >>> EmblCDROMIndexStoreTest.java:130)
> >>>
> >>> This one likely an URL not working:
> >>> org.biojava.dasobert.TestExternalSource
> >>> java.io.FileNotFoundException: http://vega.sanger.ac.uk/das/sources
> >>> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(
> >>> HttpURLConnection.java:1624)
> >>> at org.biojava.dasobert.TestExternalSource.testExternalSource(
> >>> TestExternalSource.java:51)
> >>>
> >>> org.biojava3.genome.GeneFeatureHelperTest
> >>> junit.framework.AssertionFailedError: actual file is longer
> >>> at junit.framework.Assert.fail(Assert.java:57)
> >>> at junitx.framework.FileAssert.assertBinaryEquals(FileAssert.
> >>> java:237)
> >>> at org.biojava3.genome.GeneFeatureHelperTest.
> >>> testOutputFastaSequenceLengthGFF3(GeneFeatureHelperTest.java:82)
> >>>
> >>> org.biojava3.ronn.JronnTest
> >>> java.lang.ExceptionInInitializerError: null
> >>> at java.util.Scanner.throwFor(Scanner.java:840)
> >>> at java.util.Scanner.next(Scanner.java:1461)
> >>> at java.util.Scanner.nextInt(Scanner.java:2091)
> >>> at java.util.Scanner.nextInt(Scanner.java:2050)
> >>> at
> org.biojava3.ronn.ModelLoader.loadModels(ModelLoader.java:170)
> >>> at org.biojava3.ronn.Jronn.<clinit>(Jronn.java:58)
> >>> at org.biojava3.ronn.JronnTest.verifyRanges(JronnTest.java:15)
> >>>
> >>> org.biojava3.ronn.NonstandardProteinCompoundTest
> >>> java.lang.ExceptionInInitializerError: null
> >>> at java.util.Scanner.throwFor(Scanner.java:840)
> >>> at java.util.Scanner.next(Scanner.java:1461)
> >>> at java.util.Scanner.nextInt(Scanner.java:2091)
> >>> at java.util.Scanner.nextInt(Scanner.java:2050)
> >>> at
> org.biojava3.ronn.ModelLoader.loadModels(ModelLoader.java:170)
> >>> at org.biojava3.ronn.Jronn.<clinit>(Jronn.java:58)
> >>> at
> org.biojava3.ronn.NonstandardProteinCompoundTest.testUniprot(
> >>> NonstandardProteinCompoundTest.java:56)
> >>> at org.biojava3.ronn.NonstandardProteinCompoundTest.test(
> >>> NonstandardProteinCompoundTest.java:32)
> >>>
> >>> Thanks,
> >>> George
> >>>
> >>> --------------------------------
> >>> George Waldon
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> biojava-dev mailing list
> >>> biojava-dev at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >>>
> >>
> >
> >
> >
> > --------------------------------
> > George Waldon
> >
> >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
More information about the biojava-dev
mailing list