[med-svn] r21318 - in trunk/packages/R/r-bioc-genefilter/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-01-28 10:01:56 +0000 (Thu, 28 Jan 2016)
New Revision: 21318

Added:
   trunk/packages/R/r-bioc-genefilter/trunk/debian/patches/
   trunk/packages/R/r-bioc-genefilter/trunk/debian/patches/gf_distance_definition.patch
   trunk/packages/R/r-bioc-genefilter/trunk/debian/patches/series
Modified:
   trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog
   trunk/packages/R/r-bioc-genefilter/trunk/debian/control
Log:
Apply upstream patch to fix conflicting declarations of function gf_distance


Modified: trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog	2016-01-28 09:11:14 UTC (rev 21317)
+++ trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog	2016-01-28 10:01:56 UTC (rev 21318)
@@ -1,3 +1,10 @@
+r-bioc-genefilter (1.52.0-2) unstable; urgency=medium
+
+  * Apply upstream patch to fix conflicting declarations of function gf_distance
+    Closes: #812767
+
+ -- Andreas Tille <tille at debian.org>  Thu, 28 Jan 2016 10:55:03 +0100
+
 r-bioc-genefilter (1.52.0-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-genefilter/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-genefilter/trunk/debian/control	2016-01-28 09:11:14 UTC (rev 21317)
+++ trunk/packages/R/r-bioc-genefilter/trunk/debian/control	2016-01-28 10:01:56 UTC (rev 21318)
@@ -10,7 +10,7 @@
                r-bioc-annotate,
                r-cran-survival
 Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genefilter/trunk/
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genefilter/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genefilter/trunk/
 Homepage: http://bioconductor.org/packages/release/bioc/html/genefilter.html
 

Added: trunk/packages/R/r-bioc-genefilter/trunk/debian/patches/gf_distance_definition.patch
===================================================================
--- trunk/packages/R/r-bioc-genefilter/trunk/debian/patches/gf_distance_definition.patch	                        (rev 0)
+++ trunk/packages/R/r-bioc-genefilter/trunk/debian/patches/gf_distance_definition.patch	2016-01-28 10:01:56 UTC (rev 21318)
@@ -0,0 +1,41 @@
+Origin: upstream, https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/genefilter r112947
+Author:"Morgan, Martin" <Martin.Morgan at RoswellPark.org>
+Last-Update: 2016-01-27 16:59:31
+Bug-Debian: https://bugs.debian.org/812767
+Description: bugfix: rationalize C signatures to gf_distance
+
+
+--- a/src/nd.c
++++ b/src/nd.c
+@@ -26,17 +26,14 @@
+ #if defined(USING_R) /*( R-specific stuff */
+ 
+ #define  S_CDECL
+-typedef int RSInt;
+-
+ #ifdef HAVE_CONFIG_H
+ # include <config.h>
+ #endif
+ /* we need this first to get the right options for math.h */
+ #include <R_ext/Arith.h>
+ 
+-#include <R.h>
++#include "genefilter.h"
+ #include <Rmath.h>
+-#include <Rinternals.h>
+ #include "R_ext/Error.h"
+ #include "R_ext/Applic.h" 
+ 
+--- a/src/genefilter.h
++++ b/src/genefilter.h
+@@ -2,5 +2,8 @@
+ #include <R.h>
+ #include <Rinternals.h>
+ 
+-void gf_distance(double *x, double *kval, int *nr, int *nc, double *d, 
+-		 int *diag, int *method);
++typedef int RSInt;
++
++void gf_distance(double *x, RSInt *nr, RSInt *nc, RSInt *g, double *d, 
++		 RSInt *iRow, RSInt *nInterest, RSInt *nResults, 
++		 RSInt *method, double *wval);

Added: trunk/packages/R/r-bioc-genefilter/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-genefilter/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/R/r-bioc-genefilter/trunk/debian/patches/series	2016-01-28 10:01:56 UTC (rev 21318)
@@ -0,0 +1 @@
+gf_distance_definition.patch