Package: release.debian.org Severity: normal User: release.debian....@packages.debian.org Usertags: unblock
Please unblock package fastqc I admit this upload contains a bit more than just a simple fix. In git we kept some trimming of trailing whitespace done by Jelmer Vernoo as well as his fix for the secure URI in d/copyright. Fixing the icon path in copyright as well as fixes for the syntax in debian/upstream/metadata should be sensible changes as well we did not want to remove from HEAD before the actual fix of bug #897109. So please excuse these extra but non-critical changes besides the bug fix. Thanks for working on the Buster release Andreas. unblock fastqc/0.11.8+dfsg-2 -- System Information: Debian Release: 9.9 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 4.9.0-6-amd64 (SMP w/1 CPU core) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system)
diff -Nru fastqc-0.11.8+dfsg/debian/changelog fastqc-0.11.8+dfsg/debian/changelog --- fastqc-0.11.8+dfsg/debian/changelog 2018-10-17 19:25:09.000000000 +0200 +++ fastqc-0.11.8+dfsg/debian/changelog 2019-05-21 22:20:32.000000000 +0200 @@ -1,3 +1,20 @@ +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. + + -- Dylan Aïssi <dai...@debian.org> Tue, 21 May 2019 22:20:32 +0200 + fastqc (0.11.8+dfsg-1) unstable; urgency=medium * New upstream release. @@ -9,7 +26,7 @@ fastqc (0.11.7+dfsg-1) unstable; urgency=medium [ Steffen Moeller ] - * debian/upstream/metadata: Added references to + * debian/upstream/metadata: Added references to OMICtools, SciCrunch, bio.tools registries [ Andreas Tille ] @@ -63,8 +80,8 @@ fastqc (0.11.5+dfsg-3) unstable; urgency=medium * Team upload. - - [ Canberk Koç ] + + [ Canberk Koç ] * Autopkgtest added [ Andreas Tille ] @@ -138,14 +155,14 @@ fastqc (0.11.2+dfsg-1) unstable; urgency=medium - * New upstream release + * New upstream release -- Olivier Sallou <osal...@debian.org> Mon, 09 Jun 2014 10:41:06 +0200 fastqc (0.10.1+dfsg-2) unstable; urgency=low * Add patch to fix Templates and Contaminants loading - in non interactive mode (Closes: #697604) + in non interactive mode (Closes: #697604) -- Olivier Sallou <osal...@debian.org> Wed, 05 Jun 2013 17:08:44 +0200 diff -Nru fastqc-0.11.8+dfsg/debian/copyright fastqc-0.11.8+dfsg/debian/copyright --- fastqc-0.11.8+dfsg/debian/copyright 2018-10-17 19:25:09.000000000 +0200 +++ fastqc-0.11.8+dfsg/debian/copyright 2019-05-21 22:20:32.000000000 +0200 @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: FastQC Source: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Files-Excluded: diff -Nru fastqc-0.11.8+dfsg/debian/fastqc.desktop fastqc-0.11.8+dfsg/debian/fastqc.desktop --- fastqc-0.11.8+dfsg/debian/fastqc.desktop 2018-10-17 19:25:09.000000000 +0200 +++ fastqc-0.11.8+dfsg/debian/fastqc.desktop 2019-05-21 22:20:32.000000000 +0200 @@ -3,7 +3,7 @@ Exec=fastqc GenericName[en_US]=FastQC quality control GenericName=FastQC quality control -Icon=fastqc_icon +Icon=/usr/share/icons/hicolor/32x32/apps/fastqc_icon.png Name[en_US]=FastQC quality control Name=FastQC quality control Categories=Science;Biology; diff -Nru fastqc-0.11.8+dfsg/debian/patches/htsjdk-api.patch fastqc-0.11.8+dfsg/debian/patches/htsjdk-api.patch --- fastqc-0.11.8+dfsg/debian/patches/htsjdk-api.patch 2018-10-17 19:25:09.000000000 +0200 +++ fastqc-0.11.8+dfsg/debian/patches/htsjdk-api.patch 2019-05-21 22:20:32.000000000 +0200 @@ -2,7 +2,7 @@ Author: Sascha Steinbiss <sa...@debian.org> --- a/uk/ac/babraham/FastQC/Sequence/BAMFile.java +++ b/uk/ac/babraham/FastQC/Sequence/BAMFile.java -@@ -27,7 +27,9 @@ import java.util.List; +@@ -27,7 +27,9 @@ import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; @@ -13,7 +13,7 @@ import htsjdk.samtools.SAMFormatException; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.ValidationStringency; -@@ -44,7 +46,7 @@ public class BAMFile implements Sequence +@@ -44,7 +46,7 @@ // only way to access the file pointer. private FileInputStream fis; @@ -22,22 +22,24 @@ private String name; private Sequence nextSequence = null; Iterator<SAMRecord> it; -@@ -56,11 +58,10 @@ public class BAMFile implements Sequence +@@ -56,11 +58,12 @@ name = file.getName(); this.onlyMapped = onlyMapped; - SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT); -+ SamInputResource sir = SamInputResource.of(fis); -+ SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); - -- fis = new FileInputStream(file); +- + fis = new FileInputStream(file); - - br = new SAMFileReader(fis); ++ ++ SamInputResource sir = SamInputResource.of(fis); ++ SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); ++ + br = srf.open(sir); it = br.iterator(); readNext(); -@@ -135,7 +136,7 @@ public class BAMFile implements Sequence +@@ -135,7 +138,7 @@ // through the file. if (recordSize == 0) { recordSize = (record.getReadLength()*2)+150; diff -Nru fastqc-0.11.8+dfsg/debian/tests/run-unit-test fastqc-0.11.8+dfsg/debian/tests/run-unit-test --- fastqc-0.11.8+dfsg/debian/tests/run-unit-test 2018-10-17 19:25:09.000000000 +0200 +++ fastqc-0.11.8+dfsg/debian/tests/run-unit-test 2019-05-21 22:20:32.000000000 +0200 @@ -11,6 +11,7 @@ cd $AUTOPKGTEST_TMP +set -x gunzip *.gz /usr/bin/fastqc example.fastq diff -Nru fastqc-0.11.8+dfsg/debian/upstream/edam fastqc-0.11.8+dfsg/debian/upstream/edam --- fastqc-0.11.8+dfsg/debian/upstream/edam 2018-10-17 19:25:09.000000000 +0200 +++ fastqc-0.11.8+dfsg/debian/upstream/edam 2019-05-21 22:20:32.000000000 +0200 @@ -6,9 +6,9 @@ - name: summary function: - Sequencing quality control - inputs: + input: - data: Sequence formats: [FASTQ, BAM, SAM] - outputs: + output: - data: Report formats: [Text, HTML]