[r-cran-erm] 27/33: Patches applied upstream

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-cran-erm.

commit c9717f2b32892df43aacf63b9f3889ff9dfc316f
Author: Andreas Tille <tille at debian.org>
Date:   Mon Dec 12 11:56:03 2016 +0100

    Patches applied upstream
---
 debian/changelog                           |  2 +-
 debian/patches/01_plotPWmap-fix-ranges     | 25 -----------
 debian/patches/02_plotPWmap-fix-subsetting | 70 ------------------------------
 debian/patches/series                      |  2 -
 4 files changed, 1 insertion(+), 98 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 5210298..9d9097a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,6 @@
 r-cran-erm (0.15-7-1) UNRELEASED; urgency=medium
 
-  * New upstream version
+  * New upstream version (all patches applied)
   * Take over packaging into Debian Science team
   * Consistent naming between source and binary package
 
diff --git a/debian/patches/01_plotPWmap-fix-ranges b/debian/patches/01_plotPWmap-fix-ranges
deleted file mode 100644
index 25b03c2..0000000
--- a/debian/patches/01_plotPWmap-fix-ranges
+++ /dev/null
@@ -1,25 +0,0 @@
---- a/R/plotPWmap.R
-+++ b/R/plotPWmap.R
-@@ -182,18 +182,18 @@
-   ## Now we can plot the Pathway Map
- 
-   if (pmap) { ## person map
--    xrange.pmap <- range(pfitZ,na.rm=TRUE)
-+    xrange.pmap <- range(pfitZ,finite=TRUE)
-     xrange.pmap[1] <- min(-2.5,xrange.pmap[1])
-     xrange.pmap[2] <- max(2.5,xrange.pmap[2]+1) ## need space for labels
--    yrange.pmap<-range(ploc,na.rm=TRUE)
-+    yrange.pmap<-range(ploc,finite=TRUE)
-     yrange.pmap[1]<-yrange.pmap[1]-pci*max(pse)
-     yrange.pmap[2]<-yrange.pmap[2]+pci*max(pse)
-   }
-   if (imap) { ## item map
--    xrange.imap <- range(ifitZ,na.rm=TRUE)
-+    xrange.imap <- range(ifitZ,finite=TRUE)
-     xrange.imap[1] <- min(-2.5,xrange.imap[1])
-     xrange.imap[2] <- max(2.5,xrange.imap[2]+1) ## need space for labels
--    yrange.imap<-range(iloc,na.rm=TRUE)
-+    yrange.imap<-range(iloc,finite=TRUE)
-     yrange.imap[1]<-yrange.imap[1]-ici*max(ise)
-     yrange.imap[2]<-yrange.imap[2]+ici*max(ise)
-   }
diff --git a/debian/patches/02_plotPWmap-fix-subsetting b/debian/patches/02_plotPWmap-fix-subsetting
deleted file mode 100644
index cc05f52..0000000
--- a/debian/patches/02_plotPWmap-fix-subsetting
+++ /dev/null
@@ -1,70 +0,0 @@
---- a/R/plotPWmap.R
-+++ b/R/plotPWmap.R
-@@ -86,16 +86,17 @@
-         stop("item.subset misspecified. Use 'all' or vector of at least two valid item indices/names.")
-     } else {
-       if (length(item.subset)>1 && all(item.subset %in% rownames(as.matrix(tl)))) {
--        iloc  <- iloc[item.subset]
--        ise   <- ise[item.subset]
--        ifitZ <- ifitZ[item.subset]
-         tl    <- tl[item.subset]
--
-+        keep.subset <- c()
-         for (i in rownames(as.matrix(tl)))
-           if (tl[i]==1)
-             keep.subset<-c(keep.subset,i)
-           else
-             keep.subset<-c(keep.subset,paste(i,1:tl[i],sep=":"))
-+
-+        iloc  <- iloc[keep.subset]
-+        ise   <- ise[keep.subset]
-+        ifitZ <- ifitZ[item.subset]
-         tt<-tt[keep.subset,]
-       }
-       else if(length(item.subset)!=1 || !(item.subset=="all"))
-@@ -115,16 +116,17 @@
-     }
-     else {
-       if (length(item.subset)>1 && all(item.subset %in% 1:length(tl))) {
--        iloc  <- iloc[item.subset]
--        ise   <- ise[item.subset]
--        ifitZ <- ifitZ[item.subset]
-         tl    <- tl[item.subset]
--
-+        keep.subset <- c()
-         for (i in rownames(as.matrix(tl)))
-           if (tl[i]==1)
-             keep.subset<-c(keep.subset,i)
-           else
-             keep.subset<-c(keep.subset,paste(i,1:tl[i],sep=":"))
-+
-+        iloc  <- iloc[keep.subset]
-+        ise   <- ise[keep.subset]
-+        ifitZ <- ifitZ[item.subset]
-         tt<-tt[keep.subset,]
-       }
-       else
-@@ -255,15 +257,15 @@
-       zt <- rep(ifitZ,times=tl)
- 
-     if (!horiz){
--       if (ici>0) ## draw confidence intervals
--         arrows(zt,iloc+ici*ise, zt,iloc-ici*ise, angle=90, code=3, length=0.04,
--              col=itemCI$col, lty=itemCI$lty)
--       points(zt,iloc,pch=item.pch,cex=cex.pch)
--       text(zt,iloc,rownames(tt),cex=cex.gen,pos=4)
-+      if (ici>0) ## draw confidence intervals
-+        arrows(zt,iloc+ici*ise, zt,iloc-ici*ise, angle=90, code=3, length=0.04,
-+               col=itemCI$col, lty=itemCI$lty)
-+      points(zt,iloc,pch=item.pch,cex=cex.pch)
-+      text(zt,iloc,rownames(tt),cex=cex.gen,pos=4)
-     } else {
--       if (ici>0) ## draw confidence intervals
--         arrows(iloc+ici*ise, zt,iloc-ici*ise,zt, angle=90, code=3, length=0.04,
--              col=itemCI$col, lty=itemCI$lty)
-+      if (ici>0) ## draw confidence intervals
-+        arrows(iloc+ici*ise, zt,iloc-ici*ise,zt, angle=90, code=3, length=0.04,
-+               col=itemCI$col, lty=itemCI$lty)
-       points(iloc, zt,pch=item.pch,cex=cex.pch)
-       text(iloc,zt, rownames(tt),cex=cex.gen,pos=4)
-     }
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 5105e60..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,2 +0,0 @@
-01_plotPWmap-fix-ranges
-02_plotPWmap-fix-subsetting

-- 
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