[R-sig-eco] Query related to maxent file in dismo package

Wed Sep 10 15:50:43 CEST 2014

 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
> 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 Luštrik <roman.lustrik at gmail.com>
> wrote:
>
>> 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 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:
>>>
>>> > 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 escribió:
>>> >
>>> >  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
>>> >>
>>> >>  library(rJava)
>>> >>>
>>> >> 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’
>>> >>
>>> >>  Sys.getenv("JAVA_HOME")
>>> >>>
>>> >> [1] ""
>>> >>
>>> >>> if (Sys.getenv("JAVA_HOME")!="")
>>> >>>
>>> >> +   Sys.setenv(JAVA_HOME="")
>>> >>
>>> >>> library(rJava)
>>> >>>
>>> >> 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’
>>> >>
>>> >>> Sys.setenv(JAVA_HOME="C:\\Program Files\\Java\\jre7\\")
>>> >>> options(java.home="C:\\Program Files\\Java\\jre7\\")
>>> >>> library(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 Luštrik <
>>> roman.lustrik 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 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:
>>> >>>>
>>> >>>>  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 Luštrik <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 Luštrik <
>>> roman.lustrik at gmail.com
>>> >>>>> >
>>> >>>>> wrote:
>>> >>>>>
>>> >>>>>  Do you have appropriate Java installed?
>>> >>>>>>
>>> >>>>>> Cheers,
>>> >>>>>> Roman
>>> >>>>>>
>>> >>>>>>
>>> >>>>>>
>>> >>>>>> On Fri, Sep 5, 2014 at 4:12 PM, Rajendra Mohan panda <
>>> >>>>>> rmp.iit.kgp at gmail.com> wrote:
>>> >>>>>>
>>> >>>>>>  Dear All
>>> >>>>>>>
>>> >>>>>>> Inspite of putting maxent.jar file in "dismo" package/ java
>>> folder,
>>> >>>>>>> maxent
>>> >>>>>>> is showing unavailable to run the model. I would highly
>>> appreciate
>>> >>>>>>> for
>>> >>>>>>> your
>>> >>>>>>> kind response.
>>> >>>>>>>
>>> >>>>>>>
>>> >>>>>>>
>>> >>>>>>> With best Regards
>>> >>>>>>> Rajendra M Panda
>>> >>>>>>> School of Water Resources
>>> >>>>>>> Indian Institute of Technology Kharagpur
>>> >>>>>>>
>>> >>>>>>>          [[alternative HTML version deleted]]
>>> >>>>>>>
>>> >>>>>>> _______________________________________________
>>> >>>>>>> R-sig-ecology mailing list
>>> >>>>>>> R-sig-ecology at r-project.org
>>> >>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>> >>>>>>>
>>> >>>>>>>
>>> >>>>>>
>>> >>>>>> --
>>> >>>>>> In God we trust, all others bring data.
>>> >>>>>>
>>> >>>>>>
>>> >>>>>
>>> >>>>>           [[alternative HTML version deleted]]
>>> >>>>
>>> >>>> _______________________________________________
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>>> >>>> R-sig-ecology at r-project.org
>>> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>> >>>>
>>> >>>>
>>> >>>
>>> >>> --
>>> >>> In God we trust, all others bring data.
>>> >>>
>>> >>>          [[alternative HTML version deleted]]
>>> >>
>>> >> _______________________________________________
>>> >> R-sig-ecology mailing list
>>> >> R-sig-ecology at r-project.org
>>> >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>> >>
>>> >
>>> > --
>>> > Dr Francisco Rodriguez-Sanchez
>>> > Integrative Ecology Group
>>> > Estacion Biologica de Doñana - CSIC
>>> > Avda. Americo Vespucio s/n
>>> > 41092 Sevilla (Spain)
>>> > http://sites.google.com/site/rodriguezsanchezf
>>> >
>>> >
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>>
>>
>>
>> --
>> In God we trust, all others bring data.
>>
>
>

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