[Patchwork-commits] r158 - in pkg: patchwork/R patchworkCG/R

[noreply at r-forge.r-project.org]

Author: sebastian_d
Date: 2013-01-22 16:38:54 +0100 (Tue, 22 Jan 2013)
New Revision: 158

Modified:
   pkg/patchwork/R/zzz.R
   pkg/patchworkCG/R/patchwork.CG.copynumbers.r
Log:
removed antique from bugfixing in patchworkCG

Modified: pkg/patchwork/R/zzz.R
===================================================================
--- pkg/patchwork/R/zzz.R	2013-01-21 13:57:04 UTC (rev 157)
+++ pkg/patchwork/R/zzz.R	2013-01-22 15:38:54 UTC (rev 158)
@@ -4,15 +4,15 @@
 	packageStartupMessage("Welcome to patchwork.")
 	packageStartupMessage("\n")
 	# This was an attempt to check if patchwork needed updating. It failed. Running python in onLoad is not trivial.
-	# if(system(paste("python ",getwd(),"/inst/python/vercheck.py",sep=""),intern=T) != utils::packageDescription('patchwork')$Version)
-	# 	{
-	# 	packageStartupMessage("Patchwork is not up to date, please update at:")
-	# 	packageStartupMessage("http://patchwork.r-forge.r-project.org/")
-	#   packageStartupMessage("or using: update.packages(repos="http://R-Forge.R-project.org")")
-	# 	packageStartupMessage("\n")
-	# 	}
-	# else
-	# 	{
+	if(system(paste("python ",system.file(package="patchwork"),"/python/vercheck.py",sep=""),intern=T) != utils::packageDescription('patchwork')$Version)
+		{
+		packageStartupMessage("Patchwork is not up to date, please update at:")
+		packageStartupMessage("http://patchwork.r-forge.r-project.org/")
+	  packageStartupMessage("or using: update.packages(repos=\"http://R-Forge.R-project.org\")")
+		packageStartupMessage("\n")
+		}
+	else
+		{
 		packageStartupMessage("Version: ",utils::packageDescription('patchwork')$Version)
 		packageStartupMessage("\n")
 		packageStartupMessage("If this is your first time running patchwork you should visit the")
@@ -20,5 +20,5 @@
 		packageStartupMessage("or the README file found at the install location of patchwork/inst/README")
 		packageStartupMessage("\n")
 		packageStartupMessage("Remember to keep patchwork up to date: update.packages(repos=\"http://R-Forge.R-project.org\")")
-	#	}
+		}
 	}

Modified: pkg/patchworkCG/R/patchwork.CG.copynumbers.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.copynumbers.r	2013-01-21 13:57:04 UTC (rev 157)
+++ pkg/patchworkCG/R/patchwork.CG.copynumbers.r	2013-01-22 15:38:54 UTC (rev 158)
@@ -232,15 +232,11 @@
     	distance <- Inf
     	for (cn in 0:maxCn) 
     		{
-            cat("cn: ",cn,"\n")
         	t_int <- int[paste('cn',cn,sep='')][[1]]    ## get Log-R of particular cn from 'int'
-            cat("t_int: ",t_int,"\n")
         	t_dis <- abs(regions$ratio[i]-t_int)            ## distance to that particular cn
-            cat("t_dis: ",t_dis,"\n")
         	if (t_dis < distance) 
         		{                        ## nearest so far, save.
         		distance <- t_dis -> intDist[i]
-                cat("distance: ",distance,"\n")
         		Cn[i] <- cn
         		}
     		}