[med-svn] r20365 - in trunk/packages/R/r-bioc-rsamtools/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-10-31 18:28:47 +0000 (Sat, 31 Oct 2015)
New Revision: 20365

Added:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides
Modified:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch
Log:
New upstream version, (Build-)Depends: r-bioc-biocparallel



Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2015-10-31 08:12:02 UTC (rev 20364)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2015-10-31 18:28:47 UTC (rev 20365)
@@ -1,3 +1,11 @@
+r-bioc-rsamtools (1.22.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * (Build-)Depends: r-bioc-biocparallel
+  * Add lintian-override for false positive
+
+ -- Andreas Tille <tille at debian.org>  Fri, 30 Oct 2015 14:05:41 +0100
+
 r-bioc-rsamtools (1.20.4-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/control	2015-10-31 08:12:02 UTC (rev 20364)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/control	2015-10-31 18:28:47 UTC (rev 20365)
@@ -7,8 +7,9 @@
                cdbs,
                r-base-dev,
                r-cran-bitops,
-               r-bioc-biostrings (>= 2.34.0),
-               r-bioc-genomicranges (>= 1.18.0),
+               r-bioc-biostrings (>= 2.38.0),
+               r-bioc-genomicranges (>= 1.22.0),
+               r-bioc-biocparallel,
                libbam-dev
 Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
@@ -22,7 +23,8 @@
          ${shlibs:Depends},
          r-cran-bitops,
          r-bioc-biostrings (>= 2.34.0),
-         r-bioc-genomicranges (>= 1.18.0)
+         r-bioc-genomicranges (>= 1.18.0),
+         r-bioc-biocparallel
 Recommends: r-bioc-shortread
 Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
  This package provides an interface to the 'samtools', 'bcftools', and

Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides	                        (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides	2015-10-31 18:28:47 UTC (rev 20365)
@@ -0,0 +1,2 @@
+# Same file as in source tarball is installed in binary - this does not affect reproducible builds
+r-bioc-rsamtools: package-contains-timestamped-gzip usr/lib/R/site-library/Rsamtools/unitTests/cases/ex1.sam.gz

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	2015-10-31 08:12:02 UTC (rev 20364)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch	2015-10-31 18:28:47 UTC (rev 20365)
@@ -6,11 +6,11 @@
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
 @@ -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
+ Depends: methods, S4Vectors (>= 0.7.11), IRanges (>= 2.3.7),
+         GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.21.6), XVector (>=
+         0.9.1), Biostrings (>= 2.37.1)
+-Imports: utils, BiocGenerics (>= 0.1.3), zlibbioc, bitops, BiocParallel
++Imports: utils, BiocGenerics (>= 0.1.3), bitops, BiocParallel
  Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures,
          TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db,
          TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch	2015-10-31 08:12:02 UTC (rev 20364)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch	2015-10-31 18:28:47 UTC (rev 20365)
@@ -1,3 +1,3 @@
 version=3
-opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \
+opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/bioc? \
  http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html .*/Rsamtools_([\d\.]+)\.tar\.gz