[med-svn] r23744 - in trunk/packages/R/r-bioc-aroma.light/trunk/debian: . patches

[Graham Inggs]

Author: ginggs
Date: 2017-05-15 11:26:46 +0000 (Mon, 15 May 2017)
New Revision: 23744

Modified:
   trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog
   trunk/packages/R/r-bioc-aroma.light/trunk/debian/patches/remove_test_using_external_functions.patch
Log:
Refresh remove_test_using_external_functions.patch

Modified: trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog	2017-05-15 11:23:05 UTC (rev 23743)
+++ trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog	2017-05-15 11:26:46 UTC (rev 23744)
@@ -1,6 +1,7 @@
 r-bioc-aroma.light (3.6.0-1) UNRELEASED; urgency=medium
 
   * New upstream version
+  * Refresh remove_test_using_external_functions.patch
 
  -- Graham Inggs <ginggs at debian.org>  Mon, 15 May 2017 13:14:31 +0200
 

Modified: trunk/packages/R/r-bioc-aroma.light/trunk/debian/patches/remove_test_using_external_functions.patch
===================================================================
--- trunk/packages/R/r-bioc-aroma.light/trunk/debian/patches/remove_test_using_external_functions.patch	2017-05-15 11:23:05 UTC (rev 23743)
+++ trunk/packages/R/r-bioc-aroma.light/trunk/debian/patches/remove_test_using_external_functions.patch	2017-05-15 11:26:46 UTC (rev 23744)
@@ -33,7 +33,7 @@
 -points(t(y$a), pch="+", col="blue")
 -text(t(y$a), label=expression(a[y]), adj=c(-1,0.5))
 -
--v <- c(-1,1)*10;
+-v <- c(-1,1)*10
 -xv <- list(x=x$a[1]+x$b[1]*v, y=x$a[2]+x$b[2]*v)
 -yv <- list(x=y$a[1]+y$b[1]*v, y=y$a[2]+y$b[2]*v)
 -
@@ -55,14 +55,14 @@
 -fit <- distanceBetweenLines(ax=x$a, bx=x$b, ay=y$a, by=y$b)
 -
 -xlim <- ylim <- zlim <- c(-1,3)
--dummy <- t(c(1,1,1))*100;
+-dummy <- t(c(1,1,1))*100
 -
 -# Coordinates for the lines in 3d
--v <- seq(-10,10, by=1);
+-v <- seq(-10,10, by=1)
 -xv <- list(x=x$a[1]+x$b[1]*v, y=x$a[2]+x$b[2]*v, z=x$a[3]+x$b[3]*v)
 -yv <- list(x=y$a[1]+y$b[1]*v, y=y$a[2]+y$b[2]*v, z=y$a[3]+y$b[3]*v)
 -
--for (theta in seq(30,140,length=3)) {
+-for (theta in seq(30,140,length.out=3)) {
 -  plot3d(dummy, theta=theta, phi=30, xlab="", ylab="", zlab="",
 -                             xlim=ylim, ylim=ylim, zlim=zlim)
 -
@@ -121,7 +121,7 @@
 -
 -# Plot the data with fitted lines at four different view points
 -N <- 4
--theta <- seq(0,180,length=N)
+-theta <- seq(0,180,length.out=N)
 -phi <- rep(30, length.out=N)
 -
 -# Use a different color for each set of weights
@@ -166,7 +166,7 @@
 -} # for (zzz in 0)
 -rm(zzz)
 --- a/tests/iwpca.matrix.R
-+++ b/tests/iwpca.matrix.R
++++ /dev/null
 @@ -1,76 +0,0 @@
 -library("aroma.light")
 -
@@ -192,11 +192,11 @@
 -opar <- par(mar=c(1,1,1,1)+0.1)
 -N <- 4
 -layout(matrix(1:N, nrow=2, byrow=TRUE))
--theta <- seq(0,270,length=N)
+-theta <- seq(0,270,length.out=N)
 -phi <- rep(20, length.out=N)
--xlim <- ylim <- zlim <- c(0,45);
--persp <- list();
--for (kk in seq(theta)) {
+-xlim <- ylim <- zlim <- c(0,45)
+-persp <- list()
+-for (kk in seq_along(theta)) {
 -  # Plot the data
 -  persp[[kk]] <- plot3d(y, theta=theta[kk], phi=phi[kk], xlim=xlim, ylim=ylim, zlim=zlim)
 -}
@@ -224,11 +224,11 @@
 -  yline <- matrix(c(y0,y1), nrow=length(b), ncol=2)
 -  yline <- yline + ymid
 -
--  for (kk in seq(theta)) {
+-  for (kk in seq_along(theta)) {
 -    # Set pane to draw in
--    par(mfg=c((kk-1) %/% 2, (kk-1) %% 2) + 1);
+-    par(mfg=c((kk-1) %/% 2, (kk-1) %% 2) + 1)
 -    # Set the viewpoint of the pane
--    options(persp.matrix=persp[[kk]]);
+-    options(persp.matrix=persp[[kk]])
 -
 -    # Get the first principal component
 -    points3d(t(ymid), col=col[ii])