[Debian-med-packaging] Bug#916265: picard-tools in buster FTBFS with htsjdk 2.16.1

Adrian Bunk bunk at debian.org
Wed Dec 12 11:01:14 GMT 2018


Source: picard-tools
Version: 2.8.1+dfsg-4
Severity: serious
Tags: ftbfs
Control: fixed -1 2.18.14+dfsg-1
Control: close -1

https://tests.reproducible-builds.org/debian/rb-pkg/buster/amd64/picard-tools.html

...
/build/picard-tools-2.8.1+dfsg/src/main/java/picard/sam/RevertSam.java:35: error: cannot find symbol
import htsjdk.samtools.SAMRecordUtil;
                      ^
  symbol:   class SAMRecordUtil
  location: package htsjdk.samtools
/build/picard-tools-2.8.1+dfsg/src/main/java/picard/fingerprint/GenotypeReader.java:36: error: cannot find symbol
import htsjdk.tribble.readers.LineReaderUtil;
                             ^
  symbol:   class LineReaderUtil
  location: package htsjdk.tribble.readers
/build/picard-tools-2.8.1+dfsg/src/main/java/picard/vcf/GatherVcfs.java:245: error: reference to BlockCompressedOutputStream is ambiguous
                            final BlockCompressedOutputStream blockOut = new BlockCompressedOutputStream(out, null);
                                                                         ^
  both constructor BlockCompressedOutputStream(OutputStream,File) in BlockCompressedOutputStream and constructor BlockCompressedOutputStream(OutputStream,Path) in BlockCompressedOutputStream match


This is already fixed in unstable.



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