[Biojava-dev] build errors
George Waldon
gwaldon at geneinfinity.org
Fri Jan 10 02:43:18 UTC 2014
Thank you Andreas.
The line.separator property fix solved my Jronn build error; so it is
clearly an end-of-the-line issue. I saw an "Auto Crtl convert" option
in GIT; I played with it a little bit without success during checkout.
I am using TortoiseGIT to do all this and it could be a bug there.
Since the 2 real build issues appear corrected, unless someone has a
magic fix, I'll pass on this.
Thanks again,
George
Quoting Andreas Prlic <andreas at sdsc.edu>:
> 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
>>
>
--------------------------------
George Waldon
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