Skip to content

Query related to maxent file in dismo package

11 messages · Rajendra Mohan panda, Jon Olav Skoien, Francisco Rodriguez Sanchez +2 more

#
Dear All

I have my java installed to my PC. Maxent downloaded from official site.
maxent.jar file in java folder of "dismo". Still if I check for maxent run,
it shows nonavailability to run the model. Kindly advise.

Your kind response is highly appreciated.

With best Regards
Rajendra M Panda
SWR, IIT Kharagpur, India


---------- Forwarded message ----------
From: Rajendra Mohan panda <rmp.iit.kgp at gmail.com>
Date: Fri, Sep 5, 2014 at 8:03 PM
Subject: Re: [R-sig-eco] Query related to maxent file in dismo package
To: Roman Lu?trik <roman.lustrik at gmail.com>


Dear Lustrik

I didn't get it. Kindly clarify which java you mean?

Cheers
RMP






On Fri, Sep 5, 2014 at 7:45 PM, Roman Lu?trik <roman.lustrik at gmail.com>
wrote:

  
  
#
Dear Lustrik

Thanks for your quick response. For your kind information maxent runs well
in my PC without any trouble directly but shows following error in R
me <- maxent(predictors, occtrain)
Error in .getMeVersion() : file missing:
C:/Program Files/R/R-3.1.1/library/dismo/java/maxent.jar.
Please download it here: http://www.cs.princeton.edu/~schapire/maxent/
In addition: Warning message:
In .local(x, p, ...) :
  2 (0.31%) of the presence points have NA predictor values


With best Regards
Rajendra M Panda
SWR, IIT KGP


On Fri, Sep 5, 2014 at 8:13 PM, Rajendra Mohan panda <rmp.iit.kgp at gmail.com>
wrote:

  
  
#
Well there you go. Follow the instruction in `?maxent` and put the
appropriate .jar file into the /java folder.

Cheers,
Roman


On Fri, Sep 5, 2014 at 4:48 PM, Rajendra Mohan panda <rmp.iit.kgp at gmail.com>
wrote:

  
    
#
Dear All

As you know from my trail mail, my maxent is not executing in r (working
well directly).
I think there is some java configuration problem what I see from the
following errors after using some online available codes in StackOverflow
site. Your kind advise is highly appreciated for how can I solve these
errors?
I have 64 bit PC operating system and rJava successfully installed.
utils:::menuInstallLocal()
package ?rJava? successfully unpacked and MD5 sums checked
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: fun(libname, pkgname)
  error: No CurrentVersion entry in Software/JavaSoft registry! Try
re-installing Java and make sure R and Java have matching architectures.
Error: package or namespace load failed for ?rJava?
[1] ""
+   Sys.setenv(JAVA_HOME="")
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: fun(libname, pkgname)
  error: No CurrentVersion entry in Software/JavaSoft registry! Try
re-installing Java and make sure R and Java have matching architectures.
Error: package or namespace load failed for ?rJava?
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: inDL(x, as.logical(local), as.logical(now), ...)
  error: unable to load shared object 'C:/Program
Files/R/R-3.1.1/library/rJava/libs/x64/rJava.dll':
  LoadLibrary failure:  The specified module could not be found.

Error: package or namespace load failed for ?rJava?



With best Regards
Rajendra M Panda
SWR, IIT KGP


On Fri, Sep 5, 2014 at 8:23 PM, Roman Lu?trik <roman.lustrik at gmail.com>
wrote:

  
  
2 days later
#
Which Java do you have installed?
You probably have to install Java Development Kit to be able to get 
rJava running.

Cheers,
Jon
On 9/5/2014 6:00 PM, Rajendra Mohan panda wrote:

  
    
#
Dear Rajendra,

Are you running the 64-bit version of R? In that case I think you will 
need to install the 64-bit version of Java as well, or alternatively 
switch to the 32-bit version of R to run these analyses (that is what I 
did when I had this same problem).

Try loading rJava (and dismo) with the 32-bit R version - does it work?

Hope it helps,

Paco


El 05/09/2014 18:00, Rajendra Mohan panda escribi?:

  
    
#
Dear All

I am grateful to you for your response to my queries related to maxent. I
succeeded to install rJava in 32bit R (not able to install in 64bit R).
Still maxent jar file is not executing.
My operating system is 64 bit.
Kindly advise what necessary corrections I should take keeping my 64 bit
operating system intact.
Shall I install 32 bit Java for 32bit R with operating system 64bit.
I would try but what are technical problems I do not know.
I have various options available to me by using 32bit computers of my lab
also. Each time I fail to execute maxent jar file.
I would appreciate your kind response.

Thanking you

With best Regards
Rajendra M Panda
School of Water Resources
Indian Institute of Technology Kharagpur

On Mon, Sep 8, 2014 at 7:50 PM, Francisco Rodriguez Sanchez <
f.rodriguez.sanc at gmail.com> wrote:

            

  
  
#
HI, Raj

Firstly make sure you copy and pasted maxent.jar to the folder ...\R-x.x.x\library\dismo\java, the "R-x.x.x" is your R fold.
Secondly, make sure you have administrative right to your PC.

Good luck

Li

-----Original Message-----
From: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Rajendra Mohan panda
Sent: Tuesday, 9 September 2014 2:13 PM
To: R-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] Query related to maxent file in dismo package

Dear All

I am grateful to you for your response to my queries related to maxent. I succeeded to install rJava in 32bit R (not able to install in 64bit R).
Still maxent jar file is not executing.
My operating system is 64 bit.
Kindly advise what necessary corrections I should take keeping my 64 bit operating system intact.
Shall I install 32 bit Java for 32bit R with operating system 64bit.
I would try but what are technical problems I do not know.
I have various options available to me by using 32bit computers of my lab also. Each time I fail to execute maxent jar file.
I would appreciate your kind response.

Thanking you

With best Regards
Rajendra M Panda
School of Water Resources
Indian Institute of Technology Kharagpur
On Mon, Sep 8, 2014 at 7:50 PM, Francisco Rodriguez Sanchez < f.rodriguez.sanc at gmail.com> wrote:

            
_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
----------------------------------------------------------------------------------------------------------------------------------------------------------------------
This email is intended for the addressee(s) named and may contain confidential and/or privileged information. 
If you are not the intended recipient, please notify the sender and then delete it immediately.
Any views expressed in this email are those of the individual sender except where the sender expressly and with authority states them to be the views of the NSW Office of Environment and Heritage.

PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS EMAIL
#
I solved my problem by installing Java JRE/JDK (link
<http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html>),
not "just" Java <https://java.com/en/download/index.jsp>.


On Tue, Sep 9, 2014 at 6:12 AM, Rajendra Mohan panda <rmp.iit.kgp at gmail.com>
wrote:

  
    
#
Dear All

I am very much thankful to all who have responded to my queries and also to
the forum. My special thanks to Li and Lustrik for the patience to guide me.
I am at the same time happy to inform you all that I could successfully run
maxent in 32 bit R and 32bit operating system with proper Java installation.



With best Regards
Rajendra M Panda
School of Water Resources
IIT Kharagpur

On Tue, Sep 9, 2014 at 11:48 AM, Roman Lu?trik <roman.lustrik at gmail.com>
wrote:

  
  
#
Dear Lustrik

It is possible to run maxent in 64 bit operrating system with 64 bit R only
after downloading Java from the link you provided.
However I get following error (same for both the operating systems)

me <- maxent(predictors, occtrain)
Warning message:
In .local(x, p, ...) :
  1 (0.16%) of the presence points have NA predictor values

I get output here by using predict function but no information on test gain
is there. The column showing zero values.
Am I wrong anywhere or this happens in "dismo" package.
Kindly advise.


With best Regards
Rajendra M Panda
IIT Kharagpur

On Tue, Sep 9, 2014 at 10:53 PM, Rajendra Mohan panda <rmp.iit.kgp at gmail.com