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 regression
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.

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-- 
897109: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=897109
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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

--- End Message ---
--- 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

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--- End Message ---

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