Bug#818725: picard-tools: FTBFS in unstable
Is this bug still an issue? Picard-tools has been recently updated to a
newer upstream version which builds fine for me in a current sid
pbuilder chroot.
I'm asking because the autoremoval of picard-tools due to this bug would
also drag Artemis with it...
Cheers
Sascha
On Sat, 19 Mar 2016 23:10:24 -0700 Steve Langasek wrote:
> 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 [javac] warning: [options] source value 1.5 is obsolete and will be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 [javac] warning: [options] target value 1.5 is obsolete and will be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 cannot be converted to
> List
> [javac] final List
> preAdapterDetailMetricsList = (List)
> 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 cannot be converted to
> List
> [javac] final List
> baitBiasDetailMetricsList = (List)
> 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]: *** [overr
Bug#818725: picard-tools: FTBFS in unstable
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 cannot be converted to
List
[javac] final List
preAdapterDetailMetricsList = (List)
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 cannot be converted to
List
[javac] final List baitBiasDetailMetricsList
= (List) 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.
