[Debian-med-packaging] Bug#843686: htsjdk: FTBFS: java.lang.NoSuchMethodError: net.rubygrapefruit.platform.PosixFiles.stat(Ljava/io/File; )Lnet/rubygrapefruit/platform/PosixFile
Chris Lamb
lamby at debian.org
Tue Nov 8 18:58:58 UTC 2016
Source: htsjdk
Version: 2.6.1+dfsg-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org
Dear Maintainer,
htsjdk fails to build from source in unstable/amd64:
[…]
:debianMavenPom (Thread[main,5,main]) started.
:debianMavenPom
Executing task ':debianMavenPom' (up-to-date check took 0.0 secs) due to:
No history is available.
:debianMavenPom (Thread[main,5,main]) completed. Took 0.022 secs.
:jar (Thread[main,5,main]) started.
:jar
Executing task ':jar' (up-to-date check took 0.082 secs) due to:
No history is available.
:jar (Thread[main,5,main]) completed. Took 0.516 secs.
:javadoc (Thread[main,5,main]) started.
:javadoc
Executing task ':javadoc' (up-to-date check took 0.056 secs) due to:
No history is available.
Starting process 'command '/usr/lib/jvm/java-8-openjdk-amd64/bin/javadoc''. Working directory: /home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg Command: /usr/lib/jvm/java-8-openjdk-amd64/bin/javadoc @/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/build/tmp/javadoc/javadoc.options
Successfully started process 'command '/usr/lib/jvm/java-8-openjdk-amd64/bin/javadoc''
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/vcf/VCFCompoundHeaderLine.java:85: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/vcf/VCFEncoder.java:213: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/vcf/VCFFileReader.java:82: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/vcf/VCFHeader.java:416: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/writer/BCF2Encoder.java:223: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.java:184: warning - Tag @param cannot be used in inline documentation. It can only be used in the following types of documentation: class/interface, constructor, method.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.java:184: warning - Tag @param cannot be used in inline documentation. It can only be used in the following types of documentation: class/interface, constructor, method.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.java:184: warning - Tag @param cannot be used in inline documentation. It can only be used in the following types of documentation: class/interface, constructor, method.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.java:57: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java:365: warning - @return tag cannot be used in method with void return type.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterFactory.java:247: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterFactory.java:275: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/index/interval/IntervalTree.java:69: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/index/interval/IntervalTree.java:111: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/index/Index.java:90: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/index/interval/IntervalTreeIndex.java:40: warning - @date is an unknown tag.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java:120: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java:202: warning - @ is an unknown tag.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/BlockGunzipper.java:75: warning - Parameter "compressedBlock" is documented more than once.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:526: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:369: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:365: warning - @param argument "files" is not a parameter name.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/MergingIterator.java:94: warning - Tag @see:illegal character: "60" in "java.util.Iterator<T>.hasNext"
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/MergingIterator.java:94: warning - Tag @see:illegal character: "62" in "java.util.Iterator<T>.hasNext"
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/MergingIterator.java:102: warning - Tag @see:illegal character: "60" in "java.util.Iterator<T>.next"
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/MergingIterator.java:102: warning - Tag @see:illegal character: "62" in "java.util.Iterator<T>.next"
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/SequenceUtil.java:980: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/util/SequenceUtil.java:980: warning - @return tag cannot be used in method with void return type.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/Genotype.java:143: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/Genotype.java:376: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/Genotype.java:412: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/Genotype.java:477: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/Genotype.java:538: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/Genotype.java:660: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:157: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:227: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:237: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:250: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:265: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:276: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:282: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:288: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:294: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:300: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:309: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:318: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:327: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:338: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:349: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:360: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:389: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:399: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:409: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java:417: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java:351: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java:378: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java:426: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java:448: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java:506: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java:519: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java:675: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/LazyGenotypesContext.java:147: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContext.java:469: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:220: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:232: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:271: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:287: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:296: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:352: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:361: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:370: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:380: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:392: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:405: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:415: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java:426: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/URLHelper.java:52: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/FTPHelper.java:15: warning - @date is an unknown tag.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/HTTPHelper.java:103: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/HTTPHelper.java:36: warning - @date is an unknown tag.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/LittleEndianInputStream.java:114: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/ParsingUtils.java:119: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/ParsingUtils.java:345: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/ParsingUtils.java:414: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/ParsingUtils.java:461: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/RemoteURLHelper.java:15: warning - @date is an unknown tag.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/util/URLHelper.java:34: warning - @date is an unknown tag.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/seekablestream/ISeekableStreamFactory.java:24: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/seekablestream/ISeekableStreamFactory.java:32: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/seekablestream/ISeekableStreamFactory.java:12: warning - @date is an unknown tag.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStream.java:31: warning - @date is an unknown tag.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.java:34: warning - @date is an unknown tag.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/samtools/seekablestream/SeekableStreamFactory.java:36: warning - @date is an unknown tag.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/readers/AsciiLineReader.java:118: warning - @return tag has no arguments.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/readers/LineReaderUtil.java:13: warning - @Deprecated is an unknown tag -- same as a known tag except for case.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/readers/LineReaderUtil.java:25: warning - @Deprecated is an unknown tag -- same as a known tag except for case.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/readers/LineReaderUtil.java:34: warning - @Deprecated is an unknown tag -- same as a known tag except for case.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/readers/LineReaderUtil.java:43: warning - @Deprecated is an unknown tag -- same as a known tag except for case.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/readers/LineReaderUtil.java:52: warning - @Deprecated is an unknown tag -- same as a known tag except for case.
/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/java/htsjdk/tribble/readers/TabixIteratorLineReader.java:34: warning - @date is an unknown tag.
100 warnings
:javadoc (Thread[main,5,main]) completed. Took 8.238 secs.
BUILD SUCCESSFUL
Total time: 20.242 secs
Stopped 0 compiler daemon(s).
make[1]: Leaving directory '/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg'
jh_build -O--buildsystem=gradle
debian/rules override_dh_auto_test
make[1]: Entering directory '/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg'
dh_auto_build -- test
mkdir -p .gradle/init.d
cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/
gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian test
Starting Build
Loading the Maven rules...
Settings evaluated using settings file '/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/settings.gradle'.
Projects loaded. Root project using build file '/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/build.gradle'.
Included projects: [root project 'htsjdk']
Keep-alive timer started
Adding Debian repository to project 'htsjdk'
Evaluating root project 'htsjdk' using build file '/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/build.gradle'.
Starting process 'command 'dpkg-parsechangelog''. Working directory: /home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg Command: dpkg-parsechangelog -S Version
Successfully started process 'command 'dpkg-parsechangelog''
build for version:2.6.1
Adding task debianMavenPom to project 'htsjdk'
Configuring javadoc links
All projects evaluated.
Selected primary task 'test' from project :
Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test']
:compileJava (Thread[main,5,main]) started.
:compileJava
Replacing org.apache.commons:commons-jexl:jar:2.1.1 -> org.apache.commons:commons-jexl:jar:debian
Passing through org.apache.commons:commons-parent:jar:debian
Passing through org.apache:apache:jar:debian
Replacing commons-logging:commons-logging:jar:1.1.1 -> commons-logging:commons-logging:jar:debian
Replacing org.xerial.snappy:snappy-java:jar:1.0.3-rc3 -> org.xerial.snappy:snappy-java:jar:debian
Replacing org.apache.commons:commons-compress:jar:1.4.1 -> org.apache.commons:commons-compress:jar:debian
Replacing org.tukaani:xz:jar:1.5 -> org.tukaani:xz:jar:debian
Replacing gov.nih.nlm.ncbi:ngs-java:jar:1.2.4 -> gov.nih.nlm.ncbi:ngs-java:jar:debian
Skipping task ':compileJava' as it is up-to-date (took 0.617 secs).
:compileJava UP-TO-DATE
:compileJava (Thread[main,5,main]) completed. Took 0.646 secs.
:processResources (Thread[main,5,main]) started.
:processResources
file or directory '/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg/src/main/resources', not found
Skipping task ':processResources' as it has no source files.
:processResources UP-TO-DATE
:processResources (Thread[main,5,main]) completed. Took 0.005 secs.
:classes (Thread[main,5,main]) started.
:classes
Skipping task ':classes' as it has no actions.
:classes UP-TO-DATE
:classes (Thread[main,5,main]) completed. Took 0.003 secs.
:compileTestJava (Thread[main,5,main]) started.
:compileTestJava
Replacing org.testng:testng:jar:6.9.9 -> org.testng:testng:jar:6.x
Passing through org.beanshell:bsh:jar:debian
Passing through com.beust:jcommander:jar:1.x
Executing task ':compileTestJava' (up-to-date check took 0.246 secs) due to:
No history is available.
All input files are considered out-of-date for incremental task ':compileTestJava'.
Compiling with JDK Java compiler API.
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
:compileTestJava (Thread[main,5,main]) completed. Took 5.316 secs.
:processTestResources (Thread[main,5,main]) started.
:processTestResources
Executing task ':processTestResources' (up-to-date check took 0.316 secs) due to:
No history is available.
:processTestResources (Thread[main,5,main]) completed. Took 0.662 secs.
:testClasses (Thread[main,5,main]) started.
:testClasses
Skipping task ':testClasses' as it has no actions.
:testClasses (Thread[main,5,main]) completed. Took 0.001 secs.
:test (Thread[main,5,main]) started.
:test
Executing task ':test' (up-to-date check took 0.001 secs) due to:
Task.upToDateWhen is false.
:test FAILED
:test (Thread[main,5,main]) completed. Took 0.012 secs.
FAILURE: Build failed with an exception.
* What went wrong:
Execution failed for task ':test'.
> net.rubygrapefruit.platform.PosixFiles.stat(Ljava/io/File;)Lnet/rubygrapefruit/platform/PosixFile;
* Try:
Run with --debug option to get more log output.
* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':test'.
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:69)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:46)
at org.gradle.api.internal.tasks.execution.PostExecutionAnalysisTaskExecuter.execute(PostExecutionAnalysisTaskExecuter.java:35)
at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:68)
at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:52)
at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:53)
at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:203)
at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:185)
at org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.processTask(AbstractTaskPlanExecutor.java:66)
at org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.run(AbstractTaskPlanExecutor.java:50)
at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:25)
at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:110)
at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37)
at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23)
at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43)
at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:32)
at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30)
at org.gradle.initialization.DefaultGradleLauncher$4.run(DefaultGradleLauncher.java:154)
at org.gradle.internal.Factories$1.create(Factories.java:22)
at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:90)
at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:52)
at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:151)
at org.gradle.initialization.DefaultGradleLauncher.access$200(DefaultGradleLauncher.java:32)
at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:99)
at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:93)
at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:90)
at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:62)
at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:93)
at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:82)
at org.gradle.launcher.exec.InProcessBuildActionExecuter$DefaultBuildController.run(InProcessBuildActionExecuter.java:94)
at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:43)
at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:28)
at org.gradle.launcher.exec.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:81)
at org.gradle.launcher.exec.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:46)
at org.gradle.launcher.exec.DaemonUsageSuggestingBuildActionExecuter.execute(DaemonUsageSuggestingBuildActionExecuter.java:51)
at org.gradle.launcher.exec.DaemonUsageSuggestingBuildActionExecuter.execute(DaemonUsageSuggestingBuildActionExecuter.java:28)
at org.gradle.launcher.cli.RunBuildAction.run(RunBuildAction.java:43)
at org.gradle.internal.Actions$RunnableActionAdapter.execute(Actions.java:173)
at org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:241)
at org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:214)
at org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:35)
at org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:24)
at org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:207)
at org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:169)
at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:33)
at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:22)
at org.gradle.launcher.Main.doAction(Main.java:33)
at org.gradle.launcher.bootstrap.EntryPoint.run(EntryPoint.java:45)
at org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:55)
at org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:36)
at org.gradle.launcher.GradleMain.main(GradleMain.java:23)
Caused by: java.lang.NoSuchMethodError: net.rubygrapefruit.platform.PosixFiles.stat(Ljava/io/File;)Lnet/rubygrapefruit/platform/PosixFile;
at org.gradle.internal.nativeintegration.filesystem.services.NativePlatformBackedSymlink.isSymlink(NativePlatformBackedSymlink.java:46)
at org.gradle.internal.nativeintegration.filesystem.services.GenericFileSystem.isSymlink(GenericFileSystem.java:64)
at org.gradle.api.internal.file.delete.Deleter.doDeleteInternal(Deleter.java:72)
at org.gradle.api.internal.file.delete.Deleter.delete(Deleter.java:66)
at org.gradle.api.internal.file.delete.Deleter.delete(Deleter.java:47)
at org.gradle.api.internal.file.DefaultFileOperations.delete(DefaultFileOperations.java:137)
at org.gradle.api.internal.project.AbstractProject.delete(AbstractProject.java:709)
at org.gradle.api.tasks.testing.Test.executeTests(Test.java:552)
at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:75)
at org.gradle.api.internal.project.taskfactory.AnnotationProcessingTaskFactory$StandardTaskAction.doExecute(AnnotationProcessingTaskFactory.java:228)
at org.gradle.api.internal.project.taskfactory.AnnotationProcessingTaskFactory$StandardTaskAction.execute(AnnotationProcessingTaskFactory.java:221)
at org.gradle.api.internal.project.taskfactory.AnnotationProcessingTaskFactory$StandardTaskAction.execute(AnnotationProcessingTaskFactory.java:210)
at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:585)
at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:568)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:80)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:61)
... 57 more
BUILD FAILED
Total time: 10.705 secs
Stopped 0 compiler daemon(s).
dh_auto_build: gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian test returned exit code 1
debian/rules:18: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '/home/lamby/temp/cdt.20161108185222.SOXwYGX3QV.db.htsjdk/htsjdk-2.6.1+dfsg'
debian/rules:12: recipe for target 'build' failed
make: *** [build] Error 2
[…]
The full build log is attached.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` lamby at debian.org / chris-lamb.co.uk
`-
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