From a068d13e46bcacc2a649cbc29f98fbd7b7aee204 Mon Sep 17 00:00:00 2001
From: hollorol <hollorol@gmail.com>
Date: Wed, 19 Jul 2017 23:43:37 +0200
Subject: [PATCH] fixing spinupMuso

---
 .Rhistory                                     |  4 ++
 RBBGCMuso/R/musoTime.R                        |  2 +-
 RBBGCMuso/R/spinupMuso.R                      | 38 +++++++++++++++----
 .../forarcheologists => forarcheologists      |  0
 4 files changed, 36 insertions(+), 8 deletions(-)
 rename RBBGCMuso/forarcheologists => forarcheologists (100%)

diff --git a/.Rhistory b/.Rhistory
index 3009bb5..1061708 100644
--- a/.Rhistory
+++ b/.Rhistory
@@ -4,3 +4,7 @@ install.packages("RBBGCMuso_0.1.8.tar.gz")
 install.packages("RBBGCMuso_0.1.8.tar.gz")
 install.packages("RBBGCMuso_0.1.8.tar.gz")
 install.packages("RBBGCMuso_0.2.0.0-1.tar.gz")
+install.packages("RBBGCMuso_0.2.0.0-1.tar.gz")
+library(RBBGCMuso)
+rungetMuso
+search()
diff --git a/RBBGCMuso/R/musoTime.R b/RBBGCMuso/R/musoTime.R
index 81ae587..5318a0b 100644
--- a/RBBGCMuso/R/musoTime.R
+++ b/RBBGCMuso/R/musoTime.R
@@ -24,7 +24,7 @@ isLeapyear <- function(year){
 #'@param corrigated Do you want to handle the leapyears, if yes choose TRUE
 #'@usage dayOfMonths(year, corrigated=TRUE)
 #'@return vector with 12 element. First is January, the last is December. All of the vector element represents the number of the days in that specific month
-#' @keywords internal
+#'@keywords internal
 
 
 
diff --git a/RBBGCMuso/R/spinupMuso.R b/RBBGCMuso/R/spinupMuso.R
index d06941b..4cba8b1 100644
--- a/RBBGCMuso/R/spinupMuso.R
+++ b/RBBGCMuso/R/spinupMuso.R
@@ -78,7 +78,6 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
 
     dirName<-paste(inputloc,"/LOG",sep="")
     dirERROR<-paste(inputloc,"/ERROR",sep="")
-    ERROR_EPC<-paste(inputloc,"/ERROR_EPC",sep="")
     
     if(!dir.exists(dirName)){
         dir.create(dirName)}
@@ -90,7 +89,9 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
         errorsign <- 1
     } else {
         errorsign <- 0}
-    
+
+
+
     if(keepEpc){#if keepepc option tured on
         
         if(length(unique(dirname(epc)))>1){
@@ -118,31 +119,54 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
 
         }
     }
+    
+
+
+
 
     if(debugging=="stamplog"){
         stampnum<-stamp(dirName)
-        lapply( logfiles, function (x) file.rename(from=paste(inputloc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
+        if(inputloc==outputloc){
+            lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
+            
+        } else {
+            lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
+        }
+        
         if(errorsign==1){
             lapply( logfiles, function (x) file.copy(from=paste(dirName, "/",(stampnum+1),"-",x,sep=""), to=dirERROR  ))}
 
     } else { if(debugging){
                  if(is.null(logfilename)){
-                     lapply( logfiles, function (x) file.rename(from=paste(inputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
+
+                     if(inputloc==outputloc){
+                          lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
+                     } else {
+                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName,"/", x, sep="")))     
+                     }
+
                      if(errorsign==1){
                          lapply( logfiles, function (x) file.rename(from=paste(dirName,"/", x, sep=""), to=dirERROR))
                      }
 
                  } else {
-                     lapply( logfiles, function (x) file.rename(from=paste(inputloc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))
+
+                     if(inputloc==outputloc){#These are very ugly solutions for a string problem: inputloc: "./", if outputloc equalent of inputloc, it ends with "/", the string manipulation can not handle this. The better solution is easy, but I dont have enough time(Roland Hollo's) 
+                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))                        
+                     } else {
+                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName, "/",logfilename,"-",x,sep="")))    
+                     }
+                     
                      if(errorsign==1){
                          lapply( logfiles, function (x) file.rename(from=paste(dirName, "/",logfilename,"-",x,sep=""), to=dirERROR))
                      }
                  }    
                  
              }}
+    
+    cleanupMuso(location=outputloc)
 
-
-    cleanupMuso()
+    
     if(errorsign==1){
         return("Modell Failure")
     }
diff --git a/RBBGCMuso/forarcheologists b/forarcheologists
similarity index 100%
rename from RBBGCMuso/forarcheologists
rename to forarcheologists