[med-svn] r19165 - in trunk/packages/R/r-bioc-snpstats/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-05-09 06:36:05 +0000 (Sat, 09 May 2015)
New Revision: 19165

Added:
   trunk/packages/R/r-bioc-snpstats/trunk/debian/patches/
   trunk/packages/R/r-bioc-snpstats/trunk/debian/patches/series
   trunk/packages/R/r-bioc-snpstats/trunk/debian/patches/use_debian_packaged_zlib.patch
Modified:
   trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog
   trunk/packages/R/r-bioc-snpstats/trunk/debian/control
   trunk/packages/R/r-bioc-snpstats/trunk/debian/copyright
Log:
Commit 1.16.0+dfsg-1 as uploaded to experimental


Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog	2015-05-09 06:28:03 UTC (rev 19164)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog	2015-05-09 06:36:05 UTC (rev 19165)
@@ -1,3 +1,11 @@
+r-bioc-snpstats (1.16.0+dfsg-1) experimental; urgency=medium
+
+  * New upstream version
+  * cme fix dpkg-control
+  * debian/copyright: Upstream has dropped code copies
+
+ -- Andreas Tille <tille at debian.org>  Mon, 20 Oct 2014 08:44:55 +0200
+
 r-bioc-snpstats (1.14.0+dfsg-1) unstable; urgency=medium
 
   * Initial release (closes: #756003)

Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/control	2015-05-09 06:28:03 UTC (rev 19164)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/control	2015-05-09 06:36:05 UTC (rev 19165)
@@ -2,16 +2,16 @@
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
+Testsuite: autopkgtest
 Priority: optional
-Testsuite: autopkgtest
 Build-Depends: debhelper (>= 9),
                cdbs,
                r-base-dev,
                r-cran-survival,
                r-cran-matrix,
-               r-bioc-biocgenerics,
+               r-bioc-biocgenerics (>= 0.12.0),
                zlib1g-dev
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-snpstats/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-snpstats/trunk/
 Homepage: http://bioconductor.org/packages/release/bioc/html/snpStats.html
@@ -23,7 +23,7 @@
          ${shlibs:Depends},
          r-cran-survival,
          r-cran-matrix,
-         r-bioc-biocgenerics
+         r-bioc-biocgenerics (>= 0.12.0)
 Description: BioConductor SnpMatrix and XSnpMatrix classes and methods
  This BioConductor package provides R functions to work with
  SnpMatrix and XSnpMatrix classes and methods.

Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/copyright	2015-05-09 06:28:03 UTC (rev 19164)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/copyright	2015-05-09 06:36:05 UTC (rev 19165)
@@ -2,32 +2,12 @@
 Upstream-Name: snpStats
 Upstream-Contact: David Clayton <dc208 at cam.ac.uk> 
 Source: http://bioconductor.org/packages/release/bioc/html/snpStats.html
-Files-Excluded: src/adler32.c
-                src/compress.c
-                src/crc32.c
-                src/crc32.h
-                src/deflate.c
+Files-Excluded: src/crc32.h
                 src/deflate.h
-                src/gzclose.c
-                src/gzguts.h
-                src/gzlib.c
-                src/gzread.c
-                src/gzwrite.c
-                src/infback.c
-                src/inffast.c
                 src/inffast.h
                 src/inffixed.h
-                src/inflate.c
                 src/inflate.h
-                src/inftrees.c
                 src/inftrees.h
-                src/trees.c
-                src/trees.h
-                src/uncompr.c
-                src/zconf.h
-                src/zlib.h
-                src/zutil.c
-                src/zutil.h
 
 Files: *
 Copyright: 2006-2014 David Clayton <dc208 at cam.ac.uk>

Added: trunk/packages/R/r-bioc-snpstats/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/patches/series	2015-05-09 06:36:05 UTC (rev 19165)
@@ -0,0 +1 @@
+use_debian_packaged_zlib.patch

Added: trunk/packages/R/r-bioc-snpstats/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/patches/use_debian_packaged_zlib.patch	                        (rev 0)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/patches/use_debian_packaged_zlib.patch	2015-05-09 06:36:05 UTC (rev 19165)
@@ -0,0 +1,26 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 20 Oct 2014 17:41:51 +0200
+Description: If the systems includes zlib natively there is no point in
+ requiring the import of zlibbioc
+
+
+--- a/DESCRIPTION
++++ b/DESCRIPTION
+@@ -6,7 +6,7 @@ Author: David Clayton <dc208 at cam.ac.uk>
+ Description: Classes and statistical methods for large SNP association studies, extending the snpMatrix package
+ Maintainer: David Clayton <dc208 at cam.ac.uk>
+ Depends: R(>= 2.10.0), survival, Matrix, methods
+-Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
++Imports: graphics, grDevices, stats, utils, BiocGenerics
+ Suggests: hexbin
+ License: GPL-3
+ Collate: ss.R contingency.table.R convert.R compare.R glm-test.R
+--- a/NAMESPACE
++++ b/NAMESPACE
+@@ -1,6 +1,5 @@
+ useDynLib("snpStats")
+ import(methods)
+-import(zlibbioc)
+ importFrom(graphics, abline, axis, barplot, legend, mtext, par, plot,
+            points, polygon)
+ importFrom(grDevices, heat.colors)