[med-svn] r22942 - in trunk/packages/R/r-bioc-variantannotation/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-10-27 12:42:21 +0000 (Thu, 27 Oct 2016)
New Revision: 22942

Modified:
   trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog
   trunk/packages/R/r-bioc-variantannotation/trunk/debian/control
   trunk/packages/R/r-bioc-variantannotation/trunk/debian/copyright
   trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch
   trunk/packages/R/r-bioc-variantannotation/trunk/debian/rules
Log:
  * New upstream version
  * Convert to dh-r
  * Generic BioConductor homepage



Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog	2016-10-27 12:38:39 UTC (rev 22941)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog	2016-10-27 12:42:21 UTC (rev 22942)
@@ -1,3 +1,11 @@
+r-bioc-variantannotation (1.20.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * Convert to dh-r
+  * Generic BioConductor homepage
+
+ -- Andreas Tille <tille at debian.org>  Thu, 27 Oct 2016 14:21:13 +0200
+
 r-bioc-variantannotation (1.18.0-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/control	2016-10-27 12:38:39 UTC (rev 22941)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/control	2016-10-27 12:42:21 UTC (rev 22942)
@@ -4,23 +4,22 @@
 Section: gnu-r
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               cdbs,
+               dh-r,
                r-base-dev,
                r-bioc-genomicfeatures (>= 1.22.1),
                r-bioc-bsgenome (>= 1.38.0)
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-variantannotation/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-variantannotation/trunk/
-Homepage: http://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html
+Homepage: https://bioconductor.org/packages/VariantAnnotation/
 
 Package: r-bioc-variantannotation
 Architecture: any
 Depends: ${R:Depends},
          ${misc:Depends},
          ${shlibs:Depends},
-         r-bioc-genomicfeatures (>= 1.22.0),
-         r-bioc-bsgenome (>= 1.38.0)
-Suggests: r-bioc-snpstats
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
 Description: BioConductor annotation of genetic variants
  This BioConductor package provides R functions to annotate variants,
  compute amino acid coding changess and to predict coding outcomes.

Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/copyright	2016-10-27 12:38:39 UTC (rev 22941)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/copyright	2016-10-27 12:42:21 UTC (rev 22942)
@@ -1,15 +1,15 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: VariantAnnotation
 Upstream-Contact: Valerie Obenchain <vobencha at fhcrc.org> 
-Source: http://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html
+Source: https://bioconductor.org/packages/VariantAnnotation/
 
 Files: *
-Copyright: © 2006-2014 Valerie Obenchain, Martin Morgan, Michael Lawrence
+Copyright: © 2006-2016 Valerie Obenchain, Martin Morgan, Michael Lawrence
                        with contributions from Stephanie Gogarten
 License: Artistic-2.0
 
 Files: debian/*
-Copyright: 2014 Andreas Tille <tille at debian.org>
+Copyright: 2014-2016 Andreas Tille <tille at debian.org>
 License: Artistic-2.0
 
 License: Artistic-2.0

Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch	2016-10-27 12:38:39 UTC (rev 22941)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch	2016-10-27 12:42:21 UTC (rev 22942)
@@ -11,9 +11,9 @@
  
 -import(zlibbioc)
 -
- importClassesFrom(Biobase, 
-     AssayData
- )
+ importFrom(stats, pchisq, setNames)
+ 
+ importFrom(utils, packageVersion)
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
 @@ -13,7 +13,7 @@ License: Artistic-2.0

Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/rules	2016-10-27 12:38:39 UTC (rev 22941)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/rules	2016-10-27 12:42:21 UTC (rev 22942)
@@ -1,4 +1,4 @@
 #!/usr/bin/make -f
 
-debRreposname=bioc
-include /usr/share/R/debian/r-cran.mk
+%:
+	dh $@ --buildsystem R