[med-svn] r20406 - in trunk/packages/R/r-bioc-shortread/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-11-06 10:56:51 +0000 (Fri, 06 Nov 2015)
New Revision: 20406

Added:
   trunk/packages/R/r-bioc-shortread/trunk/debian/lintian-overrides
Modified:
   trunk/packages/R/r-bioc-shortread/trunk/debian/changelog
   trunk/packages/R/r-bioc-shortread/trunk/debian/control
   trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch
   trunk/packages/R/r-bioc-shortread/trunk/debian/watch
Log:
New upstream version, ignore false lintian positives


Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/changelog	2015-11-06 10:53:49 UTC (rev 20405)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/changelog	2015-11-06 10:56:51 UTC (rev 20406)
@@ -1,3 +1,10 @@
+r-bioc-shortread (1.28.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * Ignore false positive lintian warnings
+
+ -- Andreas Tille <tille at debian.org>  Fri, 06 Nov 2015 08:59:35 +0100
+
 r-bioc-shortread (1.26.0-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/control	2015-11-06 10:53:49 UTC (rev 20405)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/control	2015-11-06 10:56:51 UTC (rev 20406)
@@ -9,7 +9,7 @@
                r-base-dev,
                r-cran-latticeextra,
                r-bioc-biobase (>= 2.26.0),
-               r-bioc-genomicalignments (>= 1.4.1),
+               r-bioc-genomicalignments (>= 1.6.0),
                r-cran-hwriter
 Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-shortread/trunk/
@@ -23,7 +23,7 @@
          ${shlibs:Depends},
          r-cran-latticeextra,
          r-bioc-biobase (>= 2.26.0),
-         r-bioc-genomicalignments (>= 1.4.1),
+         r-bioc-genomicalignments (>= 1.6.0),
          r-cran-hwriter
 Description: GNU R classes and methods for high-throughput short-read sequencing data
  This BioConductor module is a package for input, quality assessment,

Added: trunk/packages/R/r-bioc-shortread/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/lintian-overrides	                        (rev 0)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/lintian-overrides	2015-11-06 10:56:51 UTC (rev 20406)
@@ -0,0 +1,3 @@
+# Ignore false positives that are just plain copies of the gz archives in upstream tarball
+r-bioc-shortread: package-contains-timestamped-gzip usr/lib/R/site-library/ShortRead/extdata/E-MTAB-1147/.*
+r-bioc-shortread: package-contains-timestamped-gzip usr/lib/R/site-library/ShortRead/unitTests/cases/PE_export.txt.gz

Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch	2015-11-06 10:53:49 UTC (rev 20405)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch	2015-11-06 10:56:51 UTC (rev 20406)
@@ -4,17 +4,6 @@
 Description: If the systems includes zlib natively there is no point in
  requiring the import of zlibbioc
 
---- a/DESCRIPTION
-+++ b/DESCRIPTION
-@@ -18,7 +18,7 @@ Depends: BiocGenerics (>= 0.11.3), BiocP
-         2.33.14), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.28)
- Imports: Biobase, S4Vectors (>= 0.5.11), IRanges (>= 1.99.27),
-         GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.17.39), hwriter,
--        methods, zlibbioc, lattice, latticeExtra,
-+        methods, lattice, latticeExtra,
- Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
- LinkingTo: S4Vectors, IRanges, XVector, Biostrings
- biocViews: DataImport, Sequencing, QualityControl
 --- a/NAMESPACE
 +++ b/NAMESPACE
 @@ -1,6 +1,6 @@
@@ -25,3 +14,14 @@
      Biostrings, GenomeInfoDb, GenomicRanges, GenomicAlignments,
      Rsamtools, Biobase)
  
+--- a/DESCRIPTION
++++ b/DESCRIPTION
+@@ -18,7 +18,7 @@ Depends: BiocGenerics (>= 0.11.3), BiocP
+         2.37.1), Rsamtools (>= 1.21.4), GenomicAlignments (>= 1.5.4)
+ Imports: Biobase, S4Vectors (>= 0.7.1), IRanges (>= 2.3.7),
+         GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.21.6), hwriter,
+-        methods, zlibbioc, lattice, latticeExtra,
++        methods, lattice, latticeExtra,
+ Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
+ LinkingTo: S4Vectors, IRanges, XVector, Biostrings
+ biocViews: DataImport, Sequencing, QualityControl

Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/watch	2015-11-06 10:53:49 UTC (rev 20405)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/watch	2015-11-06 10:56:51 UTC (rev 20406)
@@ -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/ShortRead.html .*/ShortRead_([\d\.]+)\.tar\.gz