[med-svn] r17213 - in trunk/packages/R/r-bioc-rtracklayer/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-06-18 09:25:31 +0000 (Wed, 18 Jun 2014)
New Revision: 17213

Modified:
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
We need to wait until new dependency r-bioc-genomicalignments will be available


Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog	2014-06-18 09:13:12 UTC (rev 17212)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog	2014-06-18 09:25:31 UTC (rev 17213)
@@ -6,7 +6,11 @@
 
   [ Andreas Tille ]
   * New upstream version
+  TODO:
+    Closes: #735543  ????
   * Moved debian/upstream to debian/upstream/metadata
+  TODO: needs
+      svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicalignments/trunk/
 
  -- Andreas Tille <tille at debian.org>  Wed, 18 Jun 2014 11:11:50 +0200
 

Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control	2014-06-18 09:13:12 UTC (rev 17212)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control	2014-06-18 09:25:31 UTC (rev 17213)
@@ -13,6 +13,7 @@
                r-bioc-iranges,
                r-bioc-biostrings,
                r-bioc-genomicranges,
+               r-bioc-genomicalignments,
                r-bioc-bsgenome,
                r-bioc-rsamtools
 Standards-Version: 3.9.5
@@ -31,6 +32,7 @@
          r-bioc-iranges,
          r-bioc-biostrings,
          r-bioc-genomicranges,
+         r-bioc-genomicalignments,
          r-bioc-bsgenome,
          r-bioc-rsamtools
 Description: GNU R interface to genome browsers and their annotation tracks

Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch	2014-06-18 09:13:12 UTC (rev 17212)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch	2014-06-18 09:25:31 UTC (rev 17213)
@@ -6,21 +6,21 @@
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
 @@ -5,7 +5,7 @@ Author: Michael Lawrence, Vince Carey, R
- Depends: R (>= 2.10), methods, GenomicRanges (>= 1.13.3)
+ Depends: R (>= 2.10), methods, GenomicRanges (>= 1.15.26)
  Imports: XML (>= 1.98-0), BiocGenerics (>= 0.7.7), IRanges (>=
-         1.19.34), XVector (>= 0.1.3), GenomicRanges (>= 1.13.43),
+         1.19.34), XVector (>= 0.1.3), GenomicRanges (>= 1.15.26),
 -        Biostrings (>= 2.29.18), BSgenome (>= 1.23.1), zlibbioc, RCurl
 +        Biostrings (>= 2.29.18), BSgenome (>= 1.23.1), RCurl
-         (>= 1.4-2), Rsamtools (>= 1.13.1)
+         (>= 1.4-2), Rsamtools (>= 1.13.1), GenomicAlignments, tools
  Suggests: humanStemCell, microRNA (>= 1.1.1), genefilter, limma,
          org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19,
 --- a/NAMESPACE
 +++ b/NAMESPACE
-@@ -1,7 +1,5 @@
- useDynLib(rtracklayer, .registration = TRUE)
+@@ -6,7 +6,6 @@ useDynLib(rtracklayer, .registration = T
  
+ import(methods)
+ import(BiocGenerics)
 -import(zlibbioc)
--
- importFrom("stats", offset)
  
- importFrom(utils, count.fields)
+ ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ### base packages