Your message dated Mon, 11 Apr 2016 17:56:32 +0200
with message-id <20160411155632.gf31...@an3as.eu>
and subject line Re: Bug#818725: picard-tools: FTBFS in unstable
has caused the Debian Bug report #818725,
regarding picard-tools: FTBFS in unstable
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
818725: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=818725
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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[javac] warning: [options] source value 1.5 is obsolete and will be removed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[javac] warning: [options] target value 1.5 is obsolete and will be removed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.
--- End Message ---
--- Begin Message ---
Hi Sascha,
I hereby closing this bug since picard-tools builds fine (at least as I
can tell).
Kind regards
Andreas.
On Mon, Apr 11, 2016 at 12:30:32PM +0100, Sascha Steinbiss wrote:
> 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 <vor...@debian.org> 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<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
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
> _______________________________________________
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>
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--- End Message ---
