[med-svn] r14584 - in trunk/packages/R/r-bioc-rtracklayer/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2013-09-04 10:55:25 +0000 (Wed, 04 Sep 2013)
New Revision: 14584

Added:
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/series
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch
Modified:
   trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog
Log:
Use Debian packaged zlib


Modified: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog	2013-09-04 09:38:20 UTC (rev 14583)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog	2013-09-04 10:55:25 UTC (rev 14584)
@@ -5,8 +5,6 @@
       GenomicRanges: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/ (uploaded to new)
       Biostrings: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biostrings/trunk/       (uploaded to new)
       BSgenome:   svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-bsgenome/trunk/
-      zlibbioc:   See patches created for svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-affyio/trunk/
-                       --> these should work to avoid slibbioc
       RCurl:         http://cran.r-project.org/web/packages/RCurl/index.html
       Rsamtools:  svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
 

Added: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/series	2013-09-04 10:55:25 UTC (rev 14584)
@@ -0,0 +1 @@
+use_debian_packaged_zlib.patch

Added: 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	                        (rev 0)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/patches/use_debian_packaged_zlib.patch	2013-09-04 10:55:25 UTC (rev 14584)
@@ -0,0 +1,26 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Fri, 23 Aug 2013 12:11:49 +0200
+Description: If the systems includes zlib natively there is no point in
+ requiring the import of zlibbioc
+
+--- 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)
+ 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 @@
+ useDynLib(rtracklayer, .registration = TRUE)
+ 
+-import(zlibbioc)
+-
+ importFrom("stats", offset)
+ 
+ importFrom("XML", getNodeSet, xmlValue, xmlAttrs, htmlTreeParse,