[med-svn] r15630 - in trunk/packages/R/r-bioc-rtracklayer/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2013-12-28 00:45:07 +0000 (Sat, 28 Dec 2013)
New Revision: 15630

Modified:
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
Update patch to new version


Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control	2013-12-28 00:29:33 UTC (rev 15629)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control	2013-12-28 00:45:07 UTC (rev 15630)
@@ -11,22 +11,27 @@
                r-bioc-biocgenerics,
                r-bioc-iranges,
                r-bioc-biostrings,
-               r-bioc-genomicranges
+               r-bioc-genomicranges,
+               r-bioc-bsgenome,
+               r-bioc-rsamtools
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/
 Homepage: http://bioconductor.org/packages/release/bioc/html/rtracklayer.html
 
 Package: r-bioc-rtracklayer
-Architecture: all
+Architecture: any
 Depends: ${R:Depends},
          ${misc:Depends},
+         ${shlibs:Depends},
          r-cran-xml,
          r-cran-rcurl,
          r-bioc-biocgenerics,
          r-bioc-iranges,
          r-bioc-biostrings,
-         r-bioc-genomicranges
+         r-bioc-genomicranges,
+         r-bioc-bsgenome,
+         r-bioc-rsamtools
 Description: GNU R interface to genome browsers and their annotation tracks
  Extensible framework for interacting with multiple genome browsers
  (currently UCSC built-in) and manipulating annotation tracks in various

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	2013-12-28 00:29:33 UTC (rev 15629)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch	2013-12-28 00:45:07 UTC (rev 15630)
@@ -6,14 +6,14 @@
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
 @@ -5,7 +5,7 @@ Author: Michael Lawrence, Vince Carey, R
- Depends: R (>= 2.10), methods, GenomicRanges (>= 1.11.12)
- Imports: XML (>= 1.98-0), BiocGenerics (>= 0.1.0), IRanges (>=
-         1.15.37), GenomicRanges, Biostrings (>= 2.25.6), BSgenome (>=
--        1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.7.3)
-+        1.23.1), RCurl (>= 1.4-2), Rsamtools (>= 1.7.3)
+ Depends: R (>= 2.10), methods, GenomicRanges (>= 1.13.3)
+ Imports: XML (>= 1.98-0), BiocGenerics (>= 0.7.7), IRanges (>=
+         1.19.34), XVector (>= 0.1.3), GenomicRanges (>= 1.13.43),
+-        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)
  Suggests: humanStemCell, microRNA (>= 1.1.1), genefilter, limma,
          org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19,
-         TxDb.Hsapiens.UCSC.hg19.knownGene, hgu133plus2.db
 --- a/NAMESPACE
 +++ b/NAMESPACE
 @@ -1,7 +1,5 @@
@@ -23,4 +23,4 @@
 -
  importFrom("stats", offset)
  
- importFrom("XML", getNodeSet, xmlValue, xmlAttrs, htmlTreeParse,
+ importFrom(utils, count.fields)