[Biojava-dev] build errors

Michael Heuer heuermh at gmail.com
Thu Jan 9 06:19:34 UTC 2014 

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

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