fix the EPC bug, now the path is absolut

RBBGCMuso/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RBBGCMuso
 Title: An R package for BiomeBGC-MuSo ecosystem modelling
-Version: 0.3.2.0-0
+Version: 0.3.3.0-0
 Authors@R: person("Roland", "Hollo's", , "hollorol@gmail.com", role = c("aut", "cre"))
 Description: What the package does (one paragraph).
 Depends: R (>= 2.10)

RBBGCMuso/R/otherUsefullFunctions.R

@@ -126,6 +126,9 @@ corrigMuso <- function(settings, data){
 #' @usage file.path2(str1, str2)
 
 file.path2<-function(str1, str2){
+    if(str1==""|str1=="./"){
+        return(str2)
+    }
     str1<-file.path(dirname(str1),basename(str1))
     if(substring(str2,1,1)=="/"){
         return(paste(str1,str2,sep=""))

RBBGCMuso/R/setupMuso.R

@@ -55,6 +55,11 @@ setupMuso <- function(executable=NULL,
 
     Linuxp <-(Sys.info()[1]=="Linux")
 
+    inputParser <- function(string,fileName,counter,value=TRUE){
+        unlist(strsplit(grep(string,fileName,value=TRUE),"[\ \t]"))[counter]
+    }
+
+    
     if(is.null(inputloc)){
         inputloc<- "./"
     } else {
@@ -93,8 +98,8 @@ setupMuso <- function(executable=NULL,
     
     if(is.null(epcinput)){
         epcflag=TRUE
-        epcinput[1] <-  unlist(strsplit(grep(" EPC file name",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        epcinput[2] <-  unlist(strsplit(grep(" EPC file name",inifiles[[2]],value=TRUE),"[\ \t]"))[1]
+        epcinput[1] <-  paste0(inputloc,inputParser(string=" EPC file name",fileName=inifiles[[1]],counter=1,value=TRUE))
+        epcinput[2] <-  paste0(inputloc,inputParser(string=" EPC file name",fileName=inifiles[[2]],counter=1,value=TRUE))
     } else {
         inifiles[[1]][grep(" EPC file name",inifiles[[1]])]<-paste(epcinput[1],"\t EPC file name",sep="")