[Debian-med-packaging] Bug#917655: biojava4-live: FTBFS (cannot find symbol JAXBContext)

[Santiago Vila]

Package: src:biojava4-live
Version: 4.2.11+dfsg-1
Severity: serious
Tags: ftbfs

Dear maintainer:

I tried to build this package in buster but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep  --with javahelper
   dh_update_autotools_config -i
   dh_autoreconf -i
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/biojava4-live-4.2.11+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
sed -e 's/BJLIB/biojava4-phylo/g' debian/build.xml > biojava-phylo/build.xml

[... snipped ...]

    [javac]   location: class PeptidePropertiesImpl
    [javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:147: error: cannot find symbol
    [javac] 		JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
    [javac] 		^
    [javac]   symbol:   class JAXBContext
    [javac]   location: class PeptidePropertiesImpl
    [javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:147: error: cannot find symbol
    [javac] 		JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
    [javac] 		                  ^
    [javac]   symbol:   variable JAXBContext
    [javac]   location: class PeptidePropertiesImpl
    [javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:148: error: cannot find symbol
    [javac] 		Unmarshaller u2 = jc2.createUnmarshaller();
    [javac] 		^
    [javac]   symbol:   class Unmarshaller
    [javac]   location: class PeptidePropertiesImpl
    [javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:34: error: method does not override or implement a method from a supertype
    [javac] 	@Override
    [javac] 	^
    [javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:36: error: cannot find symbol
    [javac] 		if (ve.getSeverity() == ValidationEvent.FATAL_ERROR ||  ve.getSeverity() == ValidationEvent.ERROR){
    [javac] 		                        ^
    [javac]   symbol:   variable ValidationEvent
    [javac]   location: class MyValidationEventHandler
    [javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:36: error: cannot find symbol
    [javac] 		if (ve.getSeverity() == ValidationEvent.FATAL_ERROR ||  ve.getSeverity() == ValidationEvent.ERROR){
    [javac] 		                                                                            ^
    [javac]   symbol:   variable ValidationEvent
    [javac]   location: class MyValidationEventHandler
    [javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:37: error: cannot find symbol
    [javac] 			ValidationEventLocator  locator = ve.getLocator();
    [javac] 			^
    [javac]   symbol:   class ValidationEventLocator
    [javac]   location: class MyValidationEventHandler
    [javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java:36: error: method does not override or implement a method from a supertype
    [javac] 	@Override
    [javac] 	^
    [javac] 83 errors

BUILD FAILED
/<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/build.xml:93: Compile failed; see the compiler error output for details.

Total time: 9 seconds
make[1]: *** [debian/rules:39: override_dh_auto_build] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/biojava4-live-4.2.11+dfsg'
make: *** [debian/rules:12: build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep subprocess returned exit status 2
--------------------------------------------------------------------------------

The build was made in my autobuilder with "dpkg-buildpackage -A"
but it also fails here:

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

where you can get a full build log if you need it.

If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.

Thanks.