[Debian-med-packaging] Bug#818725: picard-tools: FTBFS in unstable

[Steve Langasek]

Package: src:picard-tools
Version: 1.138+dfsg.1-1
Severity: serious

picard-tools fails to build in a clean unstable environment with the following error:

compile-picard:
    [mkdir] Created dir: /tmp/picard-tools-1.138+dfsg.1/classes
    [javac] /tmp/picard-tools-1.138+dfsg.1/build.xml:494: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 295 source files to /tmp/picard-tools-1.138+dfsg.1/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5
    [javac] warning: [options] source value 1.5 is obsolete and will be removed in a future release
    [javac] warning: [options] target value 1.5 is obsolete and will be removed in a future release
    [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
    [javac] /tmp/picard-tools-1.138+dfsg.1/src/java/picard/illumina/parser/readers/BclQualityEvaluationStrategy.java:35: warning: '_' used as an identifier
    [javac]                 public AtomicInteger make(final Byte _) {
    [javac]                                                      ^
    [javac]   (use of '_' as an identifier might not be supported in releases after Java SE 8)
    [javac] /tmp/picard-tools-1.138+dfsg.1/src/java/picard/analysis/artifacts/ConvertSequencingArtifactToOxoG.java:56: error: incompatible types: List<MetricBase> cannot be converted to List<PreAdapterDetailMetrics>
    [javac]         final List<PreAdapterDetailMetrics> preAdapterDetailMetricsList = (List<PreAdapterDetailMetrics>) MetricsFile.readBeans(PRE_ADAPTER_IN);
    [javac]                                                                                                                                ^
    [javac] /tmp/picard-tools-1.138+dfsg.1/src/java/picard/analysis/artifacts/ConvertSequencingArtifactToOxoG.java:57: error: incompatible types: List<MetricBase> cannot be converted to List<BaitBiasDetailMetrics>
    [javac]         final List<BaitBiasDetailMetrics> baitBiasDetailMetricsList = (List<BaitBiasDetailMetrics>) MetricsFile.readBeans(BAIT_BIAS_IN);
    [javac]                                                                                                                          ^
    [javac] /tmp/picard-tools-1.138+dfsg.1/src/java/picard/sam/DownsampleSam.java:64: error: DownsamplingIterator is abstract; cannot be instantiated
    [javac]         final DownsamplingIterator iterator = new DownsamplingIterator(in.iterator(), r, PROBABILITY);
    [javac]                                               ^
    [javac] /tmp/picard-tools-1.138+dfsg.1/src/java/picard/sam/DownsampleSam.java:66: error: for-each not applicable to expression type
    [javac]         for (final SAMRecord rec : iterator) {
    [javac]                                    ^
    [javac]   required: array or java.lang.Iterable
    [javac]   found:    DownsamplingIterator
    [javac] /tmp/picard-tools-1.138+dfsg.1/src/java/picard/sam/DownsampleSam.java:73: error: cannot find symbol
    [javac]         log.info("Finished! Kept " + iterator.getKeptReads() + " out of " + iterator.getTotalReads() + " reads.");
    [javac]                                              ^
    [javac]   symbol:   method getKeptReads()
    [javac]   location: variable iterator of type DownsamplingIterator
    [javac] /tmp/picard-tools-1.138+dfsg.1/src/java/picard/sam/DownsampleSam.java:73: error: cannot find symbol
    [javac]         log.info("Finished! Kept " + iterator.getKeptReads() + " out of " + iterator.getTotalReads() + " reads.");
    [javac]                                                                                     ^
    [javac]   symbol:   method getTotalReads()
    [javac]   location: variable iterator of type DownsamplingIterator
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 6 errors
    [javac] 5 warnings

BUILD FAILED
/tmp/picard-tools-1.138+dfsg.1/build.xml:154: The following error occurred while executing this line:
/tmp/picard-tools-1.138+dfsg.1/build.xml:494: Compile failed; see the compiler error output for details.

Total time: 7 seconds
dh_auto_build: ant -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 -Djavac.target=1.5 -Ddebug=true picard-jar javadoc returned exit code 1
debian/rules:17: recipe for target 'override_dh_auto_build' failed
make[1]: *** [override_dh_auto_build] Error 2
make[1]: Leaving directory '/tmp/picard-tools-1.138+dfsg.1'
debian/rules:10: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
debuild: fatal error at line 1376:
dpkg-buildpackage -rfakeroot -D -us -uc -b failed


Possibly related to incompatibility with openjdk-8.