[med-svn] r18370 - in trunk/packages/R/r-bioc-shortread/trunk/debian: . patches tests
Andreas Tille
tille at moszumanska.debian.org
Tue Oct 21 20:37:03 UTC 2014
Author: tille
Date: 2014-10-21 20:37:03 +0000 (Tue, 21 Oct 2014)
New Revision: 18370
Modified:
trunk/packages/R/r-bioc-shortread/trunk/debian/changelog
trunk/packages/R/r-bioc-shortread/trunk/debian/control
trunk/packages/R/r-bioc-shortread/trunk/debian/copyright
trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch
trunk/packages/R/r-bioc-shortread/trunk/debian/tests/run-unit-test
Log:
New upstream version with adapted patch
Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/changelog 2014-10-21 19:00:50 UTC (rev 18369)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/changelog 2014-10-21 20:37:03 UTC (rev 18370)
@@ -1,3 +1,11 @@
+r-bioc-shortread (1.24.0-1) experimental; urgency=medium
+
+ * New upstream version
+ * cme fix dpkg-control
+ * adapt testsuite
+
+ -- Andreas Tille <tille at debian.org> Tue, 21 Oct 2014 21:21:30 +0200
+
r-bioc-shortread (1.22.0-1) unstable; urgency=medium
* New upstream version
@@ -3,8 +11,8 @@
* Moved debian/upstream to debian/upstream/metadata
* Add autopkgtest
- TODO: Needs
- svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicalignments/trunk/
+ * (Build-)Depends: r-bioc-genomicalignments
+ Closes: #753224
- -- Andreas Tille <tille at debian.org> Mon, 16 Jun 2014 23:08:56 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 24 Jul 2014 11:38:30 +0200
r-bioc-shortread (1.20.0-1) unstable; urgency=low
Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/control 2014-10-21 19:00:50 UTC (rev 18369)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/control 2014-10-21 20:37:03 UTC (rev 18370)
@@ -2,22 +2,16 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
Section: gnu-r
-Priority: optional
Testsuite: autopkgtest
+Priority: optional
Build-Depends: debhelper (>= 9),
cdbs,
r-base-dev,
r-cran-latticeextra,
- r-bioc-biobase,
- r-bioc-biocgenerics,
- r-bioc-biocparallel,
- r-bioc-genomicranges,
- r-bioc-iranges,
- r-bioc-biostrings,
- r-bioc-rsamtools,
- r-bioc-xvector,
+ r-bioc-biobase (>= 2.26.0),
+ r-bioc-genomicalignments (>= 1.2.0),
r-cran-hwriter
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-shortread/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-shortread/trunk/
Homepage: http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html
@@ -28,14 +22,8 @@
${misc:Depends},
${shlibs:Depends},
r-cran-latticeextra,
- r-bioc-biobase,
- r-bioc-biocgenerics,
- r-bioc-biocparallel,
- r-bioc-genomicranges,
- r-bioc-iranges,
- r-bioc-biostrings,
- r-bioc-rsamtools,
- r-bioc-xvector,
+ r-bioc-biobase (>= 2.26.0),
+ r-bioc-genomicalignments (>= 1.2.0),
r-cran-hwriter
Description: GNU R classes and methods for high-throughput short-read sequencing data
This BioConductor module is a package for input, quality assessment,
Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/copyright 2014-10-21 19:00:50 UTC (rev 18369)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/copyright 2014-10-21 20:37:03 UTC (rev 18370)
@@ -4,12 +4,12 @@
Source: http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html
Files: *
-Copyright: © 2006-2013 Martin Morgan, Michael Lawrence, Simon Anders
+Copyright: © 2006-2014 Martin Morgan, Michael Lawrence, Simon Anders
License: Artistic-2.0
Files: src/const.h src/maqmap_m.h
Copyright: Li Hang
-License: GPLv2
+License: GPL-2
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
@@ -29,7 +29,7 @@
Comment: The files are adapted from maq which is also packaged for Debian.
Files: debian/*
-Copyright: 2013 Andreas Tille <tille at debian.org>
+Copyright: 2013-2014 Andreas Tille <tille at debian.org>
License: Artistic-2.0
License: Artistic-2.0
Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch 2014-10-21 19:00:50 UTC (rev 18369)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch 2014-10-21 20:37:03 UTC (rev 18370)
@@ -4,24 +4,24 @@
Description: If the systems includes zlib natively there is no point in
requiring the import of zlibbioc
---- ShortRead.orig/DESCRIPTION
-+++ ShortRead/DESCRIPTION
-@@ -17,7 +17,7 @@
- Depends: BiocGenerics (>= 0.1.0), BiocParallel, Biostrings (>=
- 2.31.14), Rsamtools (>= 1.13.1), GenomicAlignments (>= 0.99.6)
- Imports: Biobase, GenomicRanges (>= 1.15.26), IRanges (>= 1.21.22),
-- hwriter, methods, zlibbioc, lattice, latticeExtra,
-+ hwriter, methods, lattice, latticeExtra,
+--- a/DESCRIPTION
++++ b/DESCRIPTION
+@@ -18,7 +18,7 @@ Depends: BiocGenerics (>= 0.11.3), BiocP
+ 2.33.14), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.28)
+ Imports: Biobase, S4Vectors (>= 0.2.2), IRanges (>= 1.99.27),
+ GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.17.39), hwriter,
+- methods, zlibbioc, lattice, latticeExtra,
++ methods, lattice, latticeExtra,
Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
- LinkingTo: IRanges, XVector, Biostrings
+ LinkingTo: S4Vectors, IRanges, XVector, Biostrings
biocViews: DataImport, Sequencing, QualityControl
---- ShortRead.orig/NAMESPACE
-+++ ShortRead/NAMESPACE
-@@ -1,7 +1,5 @@
+--- a/NAMESPACE
++++ b/NAMESPACE
+@@ -1,6 +1,6 @@
useDynLib(ShortRead, .registration=TRUE)
--import(zlibbioc)
--
- import(methods)
+-import(zlibbioc, methods, BiocGenerics, S4Vectors, IRanges,
++import(methods, BiocGenerics, S4Vectors, IRanges,
+ Biostrings, GenomeInfoDb, GenomicRanges, GenomicAlignments,
+ Rsamtools, Biobase)
- importClassesFrom(Biobase, AnnotatedDataFrame, AssayData,
Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/tests/run-unit-test 2014-10-21 19:00:50 UTC (rev 18369)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/tests/run-unit-test 2014-10-21 20:37:03 UTC (rev 18370)
@@ -1,7 +1,6 @@
#!/bin/sh -e
LC_ALL=C R --no-save <<EOT
-require("ShortRead")
-ShortRead:::.test()
+BiocGenerics:::testPackage("ShortRead")
EOT
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