Your message dated Tue, 21 May 2019 20:48:35 +0000 with message-id <e1htbgz-000etx...@fasolo.debian.org> and subject line Bug#897109: fixed in fastqc 0.11.8+dfsg-2 has caused the Debian Bug report #897109, regarding fastqc: autopkgtest fails with new version while succeeded in the past; htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed 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. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 897109: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=897109 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: fastqc Version: 0.11.7+dfsg-1 Severity: normal User: debian...@lists.debian.org Usertags: regression With the upload of version 0.11.7+dfsg-1 of fastqc, the autopkgtest¹ started to fail with the error copied below. As I have zero experience with java, I don't know what to make of this error. Could you please investigate? Paul ¹ https://ci.debian.net/packages/f/fastqc/unstable/amd64/autopkgtest [14:03:24]: test run-unit-test: [----------------------- Started analysis of example.fastq Analysis complete for example.fastq Archive: example_fastqc.zip creating: example_fastqc/ creating: example_fastqc/Icons/ creating: example_fastqc/Images/ inflating: example_fastqc/Icons/fastqc_icon.png inflating: example_fastqc/Icons/warning.png inflating: example_fastqc/Icons/error.png inflating: example_fastqc/Icons/tick.png inflating: example_fastqc/summary.txt inflating: example_fastqc/Images/per_base_quality.png inflating: example_fastqc/Images/per_tile_quality.png inflating: example_fastqc/Images/per_sequence_quality.png inflating: example_fastqc/Images/per_base_sequence_content.png inflating: example_fastqc/Images/per_sequence_gc_content.png inflating: example_fastqc/Images/per_base_n_content.png inflating: example_fastqc/Images/sequence_length_distribution.png inflating: example_fastqc/Images/duplication_levels.png inflating: example_fastqc/Images/adapter_content.png inflating: example_fastqc/fastqc_report.html inflating: example_fastqc/fastqc_data.txt inflating: example_fastqc/fastqc.fo PASS Basic Statistics example.fastq WARN Per base sequence quality example.fastq PASS Per tile sequence quality example.fastq PASS Per sequence quality scores example.fastq WARN Per base sequence content example.fastq WARN Per sequence GC content example.fastq PASS Per base N content example.fastq PASS Sequence Length Distribution example.fastq PASS Sequence Duplication Levels example.fastq WARN Overrepresented sequences example.fastq PASS Adapter Content example.fastq Failed to process toy.sam htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:373) at uk.ac.babraham.FastQC.Sequence.BAMFile.<init>(BAMFile.java:64) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:100) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:152) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:121) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316) Caused by: java.io.IOException: Stream closed at java.base/java.io.BufferedInputStream.getInIfOpen(BufferedInputStream.java:159) at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:246) at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:286) at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:345) at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:436) at htsjdk.samtools.util.BlockCompressedInputStream.isValidFile(BlockCompressedInputStream.java:351) at htsjdk.samtools.SamStreams.isBAMFile(SamStreams.java:51) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:313) ... 6 more autopkgtest [14:03:29]: test run-unit-test: -----------------------]
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--- Begin Message ---Source: fastqc Source-Version: 0.11.8+dfsg-2 We believe that the bug you reported is fixed in the latest version of fastqc, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 897...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Dylan Aïssi <dai...@debian.org> (supplier of updated fastqc package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 21 May 2019 22:20:32 +0200 Source: fastqc Architecture: source Version: 0.11.8+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Dylan Aïssi <dai...@debian.org> Closes: 897109 Changes: fastqc (0.11.8+dfsg-2) unstable; urgency=medium . * Team upload. . [ Jelmer Vernooij ] * Trim trailing whitespace. * Use secure copyright file specification URI. . [ Michael R. Crusoe ] * debian/fastqc.desktop: Update path to the icon. . [ Dylan Aïssi ] * Update d/patches/htsjdk-api.patch to fix processing of SAM/BAM files (Closes: #897109). Thanks to Chris Norman. Checksums-Sha1: 69238fd61b342a07fd7ac946b48d9ef720102305 2186 fastqc_0.11.8+dfsg-2.dsc 2ef83fe649031c5c20f6b9b6018f5b71a3ceda87 16472 fastqc_0.11.8+dfsg-2.debian.tar.xz da6b5dd5d4b2b551d8333cb35060aacc1fb1aad1 13495 fastqc_0.11.8+dfsg-2_amd64.buildinfo Checksums-Sha256: 0856ad80e15a40134957e48235b40e45f3886020fa27078bfde8b7dae2db23ed 2186 fastqc_0.11.8+dfsg-2.dsc fbd52f751b4dfd31dfc1e47d7b696fbbe65a0e10b7e59993197ae45d7235c7d0 16472 fastqc_0.11.8+dfsg-2.debian.tar.xz dfc6fc870568d9771a54dc14e2bbe965fddea3fdc5dbd848a69597f564693c09 13495 fastqc_0.11.8+dfsg-2_amd64.buildinfo Files: 57eb3d71907d6e609617fe30b3dc4d05 2186 science optional fastqc_0.11.8+dfsg-2.dsc 37d010b7f300cad240bbe97cca92cf89 16472 science optional fastqc_0.11.8+dfsg-2.debian.tar.xz b145c8796b0ac0fdf4b54bb3583a7c2c 13495 science optional fastqc_0.11.8+dfsg-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEmjwHvQbeL0FugTpdYS7xYT4FD1QFAlzkX7cSHGRhaXNzaUBk ZWJpYW4ub3JnAAoJEGEu8WE+BQ9Uu8IP/3owqQ59QyYY6RWLO6UE1wEfz2QBxfqx mdFV6kvUo0KYfXeE8O0GKRfcaSsbNDE4h3hlSVgtts8027i8FgSLqkAJ/Fhfkf1H Z6BILL5irYT7a76VpOXKa1fr9UjJQJ4DcThsh2K3sz+WJqzRKigx94eZvj76CSXZ v019lD9Pw8oDLes+/sFCS70AQrjT01O5sV7w9CbDgRqdWvk83hQEgwM8cwzQNmnw 1cjIssRoMyLLE3Q17EFftWKybg1zRvYLL8SCiVi09OIw0Rk6Uq3K1mY14o7GjCbU Er4fko+KpCxbfaLmrVpwAgePgnD5HLVs0Ll9WYrRWrwaJpBgwagJ9TJ/UFOH+eEu RB/j3eHohCX53AJIHlQT9nyCip9X8IYbGa1NZH9q5wsD9iIRDWqtptRbBAxfOPxD tcJqfUOaV+hsg+N8bX+z3rUaCuAPT2Vmgj5Cru20L+T/L157WFby+QDwtQX92qMt 6zRt/qPwv325oDSRanc9lBnipanUGk+wwtl4/LVuRyHDG0R/7madFl2q+t7nBBCN YmW7amzIbUX4yDCqCHzUa+5g6cwXnWVcn6nFZTj0Cn3RkXrK2EVrku2NAnyMbTvm v+o6ZjI7/TXLl99EFRD9QTiELsAJxgFc62ynD3Rdk3EHfsOmZYre/S0EBJo0j3Jt Z2imAd0ioS2t =oBoT -----END PGP SIGNATURE-----
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