[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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