[R] Maxent Jarfile

[Annemarie Fischer]

Hi,
I have been trying to solve the below problem for 2 days with no success. Hopefully you can help as i can find no assistance online.
I am attempting to run the niche.equivalency.test and the bg.similarity.test using RStudio and Maxent. I keep getting the error:
Error: Unable to access jarfile C:/ProgramError in file(fname, "r") : cannot open the connectionIn addition: Warning messages:1: running command 'java -jar C:/Program Files/R/R-3.1.3/library/dismo/java/maxent.jar -e  R.phyloclim.temp/background.csv -s  R.phyloclim.temp/samples.csv -j  R.phyloclim.temp/proj/ -o  R.phyloclim.temp/out/  -r removeduplicates nopictures autorun' had status 1 2: In file(fname, "r") :  cannot open file 'R.phyloclim.temp/out/Rhinolophus blasii_proj.asc': No such file or directory
I suspect the issue is that the file directory doesnt have "", but i have no idea how to add these in, as in RStudio values, the "" does appear.
My code is:
# load required packageslibrary(raster)library(mgcv)library(dismo)library(rgdal)library(ellipse)library(sp)library(proj4)library(rgeos)    library(rJava)library(maptools)library(rasterVis)library(phyloclim)
# path to MAXENT# --------------maxent.exe <- paste(system.file(package="dismo"),                     "/java/maxent.jar", sep = "")
# a data frame of coordinates where two species # have been detected ('presence points') and# a raster stack of environmental covariables# --------------------------------------
###Change to correct species usedfile <- paste(system.file(package="dismo"), "/ex/Rhinolophus_species.csv", sep="")# this is the file we will use:file
#save(file, file="Molossidae_rarefied_points.rda")
#data()#data(package = .packages(all.available = TRUE))
#myData <- read.csv("file", header=TRUE, nrows=10000)
Rhinolophus_species <- read.table(file, header=TRUE, sep=',')
species <- c("Rhinolophus blasii", "Rhinolophus clivosus")#data(sites)samples <- Rhinolophus_species[grep(paste(species, collapse = "|"), Rhinolophus_species$Spp), ]data.path <- system.file("extdata", package = "phyloclim")preds <- list.files(path = data.path, pattern = "[.]asc")preds <- paste(data.path, preds, sep = "/")preds <- stack(lapply(X = preds, FUN = raster))
# testing against 9 permutations of the data# -------------------------------------------reps <- 1000
# run hypothesis tests# --------------------if (file.exists(maxent.exe)){  net <- niche.equivalency.test(samples, preds, reps, maxent.exe)  net; plot(net)  bst <- bg.similarity.test(samples, preds, reps, app = maxent.exe)  bst; plot(bst)} else {  message("get a copy of MAXENT (see Details)")} 		 	   		  
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