[Debian-med-packaging] Bug#843712: biojava4-live: FTBFS (failing tests)

[Santiago Vila]

Package: src:biojava4-live
Version: 4.1.0+dfsg-3
Severity: serious

Dear maintainer:

I tried to build this package in stretch with "dpkg-buildpackage -A"
(which is what the "Arch: all" autobuilder would do to build it)
but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep  --with javahelper
   dh_testdir -i
   dh_update_autotools_config -i
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/biojava4-live-4.1.0+dfsg'
dh_auto_configure
sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml
sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml
sed -e 's/BJLIB/biojava4-core/g' debian/build.xml > biojava-core/build.xml
sed -e 's/BJLIB/biojava4-alignment/g' debian/build.xml > biojava-alignment/build.xml
sed -e 's/BJLIB/biojava4-genome/g' debian/build.xml > biojava-genome/build.xml
sed -e 's/BJLIB/biojava4-modfinder/g' debian/build.xml > biojava-modfinder/build.xml

[... snipped ...]

    [junit] Testcase: testProteinSequenceFactoring[0] took 0 sec
    [junit] Testcase: testFeatures[0] took 0 sec
    [junit] Testcase: testProteinSequenceFactoring[1] took 0 sec
    [junit] Testcase: testFeatures[1] took 0 sec
    [junit] Testcase: testProteinSequenceFactoring[2] took 0 sec
    [junit] Testcase: testFeatures[2] took 0 sec
    [junit] Testcase: testProteinSequenceFactoring[3] took 0 sec
    [junit] Testcase: testFeatures[3] took 0 sec
    [junit] Testcase: testProteinSequenceFactoring[4] took 0 sec
    [junit] Testcase: testFeatures[4] took 0 sec
    [junit] Testcase: testProteinSequenceFactoring[5] took 0 sec
    [junit] Testcase: testFeatures[5] took 0 sec
    [junit] Testcase: testProteinSequenceFactoring[6] took 0 sec
    [junit] Testcase: testFeatures[6] took 0 sec
    [junit] Testcase: testProteinSequenceFactoring[7] took 0 sec
    [junit] Testcase: testFeatures[7] took 0 sec
    [junit] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
    [junit] Testsuite: org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
    [junit] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.592 sec
    [junit] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.592 sec
    [junit] ------------- Standard Error -----------------
    [junit] SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
    [junit] SLF4J: Defaulting to no-operation (NOP) logger implementation
    [junit] SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
    [junit] ------------- ---------------- ---------------
    [junit] 
    [junit] Testcase: testWrongSequence took 0.554 sec
    [junit] 	Caused an ERROR
    [junit] Unexpected exception, expected<java.io.IOException> but was<org.biojava.nbio.core.exceptions.ParserException>
    [junit] java.lang.Exception: Unexpected exception, expected<java.io.IOException> but was<org.biojava.nbio.core.exceptions.ParserException>
    [junit] Caused by: org.biojava.nbio.core.exceptions.ParserException: Section key was null
    [junit] 	at org.biojava.nbio.core.sequence.io.GenbankSequenceParser.parse(GenbankSequenceParser.java:143)
    [junit] 	at org.biojava.nbio.core.sequence.io.GenbankSequenceParser.getSequence(GenbankSequenceParser.java:368)
    [junit] 	at org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader.<init>(GenbankProxySequenceReader.java:86)
    [junit] 	at org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest.testWrongSequence(SimpleGenbankProxySequenceReaderTest.java:53)
    [junit] 

BUILD FAILED
/<<BUILDDIR>>/biojava4-live-4.1.0+dfsg/biojava-core/build.xml:101: Test org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest failed

Total time: 13 seconds
debian/rules:57: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/biojava4-live-4.1.0+dfsg'
debian/rules:10: recipe for target 'build-indep' failed
make: *** [build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2
--------------------------------------------------------------------------------

For a full build log please see:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/biojava4-live.html

Note: Even if this package is Arch:all, please consider uploading in
source-only form, so that we get official build logs available here:

https://buildd.debian.org/status/package.php?p=biojava4-live

Thanks.