[med-svn] r19208 - in trunk/packages/R/r-bioc-rsamtools/trunk/debian: . patches tests

[Andreas Tille]

Author: tille
Date: 2015-05-11 10:01:41 +0000 (Mon, 11 May 2015)
New Revision: 19208

Added:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/control
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
New upstream version, Activate autopkgtest



Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test	2015-05-11 09:28:11 UTC (rev 19207)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test	2015-05-11 10:01:41 UTC (rev 19208)
@@ -9,7 +9,7 @@
 BiocGenerics:::testPackage('Rsamtools')
 EOT
 
-Currently one our of 73 tests is failing which is sorted out with
+Currently one out of 73 tests is failing which is sorted out with
 upstream before an autopkgtest will be provided.
 
  -- Andreas Tille <tille at debian.org>  Mon, 16 Jun 2014 16:28:55 +0200

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2015-05-11 09:28:11 UTC (rev 19207)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2015-05-11 10:01:41 UTC (rev 19208)
@@ -1,3 +1,10 @@
+r-bioc-rsamtools (1.20.1-1) unstable; urgency=medium
+
+  * New upstream version
+  * Activate autopkgtest
+
+ -- Andreas Tille <tille at debian.org>  Mon, 11 May 2015 11:34:17 +0200
+
 r-bioc-rsamtools (1.18.0-1) experimental; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch	2015-05-11 09:28:11 UTC (rev 19207)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch	2015-05-11 10:01:41 UTC (rev 19208)
@@ -5,10 +5,10 @@
 
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
-@@ -15,7 +15,7 @@ LazyLoad: yes
- Depends: methods, IRanges (>= 1.21.10), GenomicRanges (>= 1.15.11),
-         XVector (>= 0.3.2), Biostrings (>= 2.31.3), GenomeInfoDb(>=
-         0.99.17)
+@@ -17,7 +17,7 @@ LazyLoad: yes
+ Depends: methods, S4Vectors (>= 0.5.11), IRanges (>= 1.99.17),
+         GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.17.19), XVector
+         (>= 0.5.3), Biostrings (>= 2.33.11)
 -Imports: utils, BiocGenerics (>= 0.1.3), zlibbioc, bitops
 +Imports: utils, BiocGenerics (>= 0.1.3), bitops
  Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures,
@@ -22,6 +22,6 @@
  
 -import(zlibbioc)
 -
- import(XVector)
+ importFrom(bitops, bitAnd)
  
- importFrom(bitops, bitAnd)
+ importFrom(utils, read.table)           # normalizePath --> base in R-2.13

Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/control	2015-05-11 10:01:41 UTC (rev 19208)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-bioc-shortread
+Restrictions: allow-stderr

Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/run-unit-test	2015-05-11 10:01:41 UTC (rev 19208)
@@ -0,0 +1,6 @@
+#!/bin/sh -e
+
+LC_ALL=C R --no-save <<EOT
+BiocGenerics:::testPackage('Rsamtools')
+EOT
+