[med-svn] r23271 - in trunk/packages/R/r-cran-treescape/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-12-08 15:31:54 +0000 (Thu, 08 Dec 2016)
New Revision: 23271

Added:
   trunk/packages/R/r-cran-treescape/trunk/debian/patches/
   trunk/packages/R/r-cran-treescape/trunk/debian/patches/0001-fixing-issue-with-new-release-of-ape.patch
   trunk/packages/R/r-cran-treescape/trunk/debian/patches/series
Modified:
   trunk/packages/R/r-cran-treescape/trunk/debian/changelog
   trunk/packages/R/r-cran-treescape/trunk/debian/compat
   trunk/packages/R/r-cran-treescape/trunk/debian/control
   trunk/packages/R/r-cran-treescape/trunk/debian/watch
Log:
  * Fix issue with new release of ape
    Closes: #845753
  * debhelper 10
  * d/watch: version=4



Modified: trunk/packages/R/r-cran-treescape/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-cran-treescape/trunk/debian/changelog	2016-12-08 14:56:25 UTC (rev 23270)
+++ trunk/packages/R/r-cran-treescape/trunk/debian/changelog	2016-12-08 15:31:54 UTC (rev 23271)
@@ -1,3 +1,12 @@
+r-cran-treescape (1.10.17-2) unstable; urgency=medium
+
+  * Fix issue with new release of ape
+    Closes: #845753
+  * debhelper 10
+  * d/watch: version=4
+
+ -- Andreas Tille <tille at debian.org>  Thu, 08 Dec 2016 16:01:06 +0100
+
 r-cran-treescape (1.10.17-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-cran-treescape/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-cran-treescape/trunk/debian/compat	2016-12-08 14:56:25 UTC (rev 23270)
+++ trunk/packages/R/r-cran-treescape/trunk/debian/compat	2016-12-08 15:31:54 UTC (rev 23271)
@@ -1 +1 @@
-9
+10

Modified: trunk/packages/R/r-cran-treescape/trunk/debian/control
===================================================================
--- trunk/packages/R/r-cran-treescape/trunk/debian/control	2016-12-08 14:56:25 UTC (rev 23270)
+++ trunk/packages/R/r-cran-treescape/trunk/debian/control	2016-12-08 15:31:54 UTC (rev 23271)
@@ -3,7 +3,7 @@
 Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
                dh-r,
                r-base-dev,
                r-cran-ape,

Added: trunk/packages/R/r-cran-treescape/trunk/debian/patches/0001-fixing-issue-with-new-release-of-ape.patch
===================================================================
--- trunk/packages/R/r-cran-treescape/trunk/debian/patches/0001-fixing-issue-with-new-release-of-ape.patch	                        (rev 0)
+++ trunk/packages/R/r-cran-treescape/trunk/debian/patches/0001-fixing-issue-with-new-release-of-ape.patch	2016-12-08 15:31:54 UTC (rev 23271)
@@ -0,0 +1,35 @@
+From: thibautjombart <thibautjombart at gmail.com>
+Date: Fri, 2 Dec 2016 17:09:52 +0000
+Subject: [PATCH 1/3] fixing issue with new release of ape
+
+---
+ vignettes/DengueVignette.Rmd                      |     9 +-
+
+--- a/vignettes/DengueVignette.Rmd
++++ b/vignettes/DengueVignette.Rmd
+@@ -97,6 +97,8 @@ Create bootstrap trees:
+ DMLboots <- bootstrap.pml(Dfit, optNni=TRUE)
+ # root:
+ DMLbootsrooted <- lapply(DMLboots, function(x) root(x, resolve.root=TRUE, outgroup="D4Thai63"))
++class(DMLbootsrooted) <- "multiPhylo"
++
+ ```
+ 
+ Plot the ML tree again, with bootstrap support values:
+@@ -112,6 +114,7 @@ We now use the function `treescape` to f
+ ```{r run_treescape}
+ # collect the trees into a single object of class multiPhylo:
+ DengueTrees <- c(BEASTtrees,Dnjboots$trees,DMLbootsrooted,list(DnjRooted),list(DfitTreeRooted))
++DengueTrees <- c(BEASTtrees,Dnjboots$trees,DMLbootsrooted,DnjRooted,DfitTreeRooted)
+ class(DengueTrees) <- "multiPhylo"
+ # add tree names:
+ names(DengueTrees)[1:200] <- paste0("BEAST",1:200)
+@@ -267,7 +270,7 @@ We used TreeAnnotator (Drummond and Ramb
+ # load the MCC tree
+ data(DengueBEASTMCC)
+ # concatenate with other BEAST trees
+-BEAST201 <- c(BEASTtrees,list(DengueBEASTMCC))
++BEAST201 <- c(BEASTtrees, DengueBEASTMCC)
+ # compare using treescape:
+ BEASTscape <- treescape(BEAST201, nf=5)
+ # simple plot:

Added: trunk/packages/R/r-cran-treescape/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-cran-treescape/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/R/r-cran-treescape/trunk/debian/patches/series	2016-12-08 15:31:54 UTC (rev 23271)
@@ -0,0 +1 @@
+0001-fixing-issue-with-new-release-of-ape.patch

Modified: trunk/packages/R/r-cran-treescape/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-cran-treescape/trunk/debian/watch	2016-12-08 14:56:25 UTC (rev 23270)
+++ trunk/packages/R/r-cran-treescape/trunk/debian/watch	2016-12-08 15:31:54 UTC (rev 23271)
@@ -1,3 +1,3 @@
-version=3
+version=4
 http://cran.r-project.org/src/contrib/treescape_([-0-9\.]*).tar.gz