- up to 1.14.2

diff --git a/R-Rsamtools.spec b/R-Rsamtools.spec
index 26cfe10ae9c63383e13b22fc6333baeb888ad8fc..3385420792a39184927c207b5ddaeb7ef7bda4cc 100644 (file)
--- a/R-Rsamtools.spec
+++ b/R-Rsamtools.spec
@@ -2,14 +2,14 @@
 
 Summary:       Binary alignment (BAM), variant call (BCF), or tabix file import
 Name:          R-%{packname}
-Version:       1.12.4
+Version:       1.14.2
 Release:       1
 License:       Artistic 2.0
 Group:         Applications/Math
-Source0:       http://www.bioconductor.org/packages/2.12/bioc/src/contrib/%{packname}_%{version}.tar.gz
-# Source0-md5: 75189a4203fb3eb9bd8cda03f3e8c523
+Source0:       http://www.bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz
+# Source0-md5: 83aa5c41214583f83c86bcc90355d59e
 Patch0:                bogus-deps.patch
-URL:           http://www.bioconductor.org/packages/2.12/bioc/html/Rsamtools.html
+URL:           http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html
 BuildRequires: R
 BuildRequires: R-IRanges-devel >= 1.15.35
 BuildRequires: R-GenomicRanges >= 1.11.38

diff --git a/bogus-deps.patch b/bogus-deps.patch
index 5b575c5b4a7457c415bd550cf3a8a3346c709835..52b0a28b54840b71b9834d450df4241f36229d7e 100644 (file)
--- a/bogus-deps.patch
+++ b/bogus-deps.patch
@@ -2,13 +2,13 @@
 +++ Rsamtools/Rsamtools/DESCRIPTION    2013-05-10 14:30:55.269037518 +0200
 @@ -14,7 +14,7 @@
  LazyLoad: yes
- Depends: methods, IRanges (>= 1.15.35), GenomicRanges (>= 1.11.38),
-         Biostrings (>= 2.25.6)
--Imports: methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc,
-+Imports: methods, utils, IRanges, GenomicRanges, Biostrings,
-         bitops, BiocGenerics (>= 0.1.3)
- Suggests: ShortRead (>= 1.13.19), GenomicFeatures,
-         TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, pasillaBamSubset,
+ Depends: methods, IRanges (>= 1.19.11), GenomicRanges (>= 1.13.35),
+         XVector, Biostrings (>= 2.29.7)
+-Imports: utils, BiocGenerics (>= 0.1.3), zlibbioc, bitops
++Imports: utils, BiocGenerics (>= 0.1.3), bitops
+ Suggests: ShortRead (>= 1.19.10), GenomicFeatures,
+         TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db,
+         TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
 --- Rsamtools/Rsamtools/NAMESPACE~     2013-04-04 00:15:29.000000000 +0200
 +++ Rsamtools/Rsamtools/NAMESPACE      2013-05-10 14:31:12.692547009 +0200
 @@ -1,7 +1,5 @@
@@ -16,6 +16,6 @@
  
 -import(zlibbioc)
 -
- importFrom(bitops, bitAnd)
+ import(XVector)
  
- importFrom(utils, read.table)           # normalizePath --> base in R-2.13
+ importFrom(bitops, bitAnd)