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)")}
[[alternative HTML version deleted]]
Hi Annemarie, You have sent the email in HTML and it is very close to unreadable. Could you please resubmit the message in plain text. R-help does not accept HTML and, as happened here, the text gets seriously mangled. John Kane Kingston ON Canada> -----Original Message----- > From: annemarie_dh at hotmail.com > Sent: Wed, 8 Jul 2015 20:22:57 +0000 > To: r-help at r-project.org > Subject: [R] Maxent Jarfile > > 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 requiredpackageslibrary(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)")} > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
?Hi John,? Sorry about that. Please find attached the code, error and input file. Thanks, Annemarie ? Original Message ? From: John Kane Sent: Thursday 9 July 2015 00:26 To: Annemarie Fischer; r-help at r-project.org Subject: Re: [R] Maxent Jarfile Hi Annemarie, You have sent the email in HTML and it is very close to unreadable. Could you please resubmit the message in plain text. R-help does not accept HTML and, as happened here, the text gets seriously mangled. John Kane Kingston ON Canada> -----Original Message----- > From: annemarie_dh at hotmail.com > Sent: Wed, 8 Jul 2015 20:22:57 +0000 > To: r-help at r-project.org > Subject: [R] Maxent Jarfile > > 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 requiredpackageslibrary(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)")} > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.____________________________________________________________ ______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
You would do better to contact the package owner for this, as it's a
problem specific to the package. In this case the problem looks to be
in dismo, so you should use packageDescription("dismo") to discover
that Robert Hijmans is the person to contact. I would suggest running
maxent() first to see if it works. If it does then the problem is
elsewhere, so use find("niche.equivalency.test") to find out what
package that function is in, and email the maintainer of that package
for help.
Oh, and also read the posting guide:
<http://www.r-project.org/posting-guide.html> :-)
Bob
(who is not going to wait 15 hours to send this)
On 8 July 2015 at 22:22, Annemarie Fischer <annemarie_dh at hotmail.com>
wrote:> 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)")}
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Bob O'Hara
Biodiversity and Climate Research Centre
Senckenberganlage 25
D-60325 Frankfurt am Main,
Germany
Tel: +49 69 798 40226
Mobile: +49 1515 888 5440
WWW: http://www.bik-f.de/root/index.php?page_id=219
Blog: http://occamstypewriter.org/boboh/
Journal of Negative Results - EEB: www.jnr-eeb.org