Source: htsjdk Version: 2.6.1+dfsg-1 Severity: serious Justification: fails to build from source User: reproducible-bui...@lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-bui...@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 `. `'` la...@debian.org / chris-lamb.co.uk `-
htsjdk.2.6.1+dfsg-1.unstable.amd64.log.txt.gz
Description: Binary data