Package: src:fastqc Version: 0.11.8+dfsg-1 Severity: important Tags: sid buster
fastqc fails it's autopkg tests according to https://ci.debian.net/data/packages/unstable/amd64/f/fastqc/latest-autopkgtest/log.gz ailed to process toy.sam htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:448) at uk.ac.babraham.FastQC.Sequence.BAMFile.<init>(BAMFile.java:64) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:100) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:152) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:121) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316) Caused by: java.io.IOException: Stream closed at java.base/java.io.BufferedInputStream.getInIfOpen(BufferedInputStream.java:165) at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:252) at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:292) at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:351) at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:583) at htsjdk.samtools.util.BlockCompressedInputStream.isValidFile(BlockCompressedInputStream.java:443) at htsjdk.samtools.SamStreams.isBAMFile(SamStreams.java:51) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:374) ... 6 more autopkgtest [08:36:51]: test run-unit-test: -----------------------] autopkgtest [08:36:51]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - run-unit-test FAIL non-zero exit status 1 autopkgtest [08:36:51]: @@@@@@@@@@@@@@@@@@@@ summary
