[Biomod-commits] Maxent probelm

[Damien Georges]

Dear Gabriele,

It seems to have an issue under Windows OS in path to maxent.jar file 
construction.. I will try to solve it ASAP.

The last thing you can try is to define a empty path (equivalent to 
getwd() ) in MAXENT modelling options.

myBiomodOption <- BIOMOD_ModelingOptions(MAXENT = list( 
path_to_maxent.jar = ""))


If this not solve the issue, you will have to wait for the ( coming soon 
)  biomod2 release...

Cheers,

Damien.


On 22/11/2012 09:36, Gabriele Casazza wrote:
> Dear Damien,
> yes, file.exists("maxent.jar") command returns TRUE while, 
> system("java -jar maxent.jar") opened Maxent in another window but R 
> crashed.
> system(command=paste("java -mx512m -jar ", 
> file.path(myBiomodOption at MAXENT$path_to_maxent.jar, "maxent.jar"))) is 
> unable to open Maxent.
> All others alghritms run without problems.
>
> Thank you so much for the help
> Gabriele
>
>
>
> I attach the R commands and the results:
>
> > file.exists("maxent.jar")
> [1] TRUE
> > myBiomodOption <- BIOMOD_ModelingOptions(MAXENT = list( 
> path_to_maxent.jar = getwd()))
> >
> > myBiomodModelOut <- BIOMOD_Modeling(
> + myBiomodData,
> + models = 'MAXENT',
> + models.options = myBiomodOption,
> + NbRunEval=1,
> + DataSplit=80,
> + Yweights=NULL,
> + VarImport=1,
> + models.eval.meth = c("TSS","ROC", "KAPPA"),
> + SaveObj = TRUE,
> + rescal.all.models = T)
>
>
> Loading required library...
>
> Checking Models arguments...
>
> Creating suitable Workdir...
>
>                         ! Weights where defined to rise a 0.5 
> prevalence !
>
> -=-=-=-  Pallionii  Modeling Summary 
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> 8  environmental variables ( bio2 bio3 bio7 bio9 bio15 bio18 bio19 
> substr )
> Number of evaluation repetitions : 2
> Models selected : MAXENT
> Total number of model runs : 2
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 
>
>
>
> -=-=-=- Run :  Pallionii_PA1
>
>
> -=-=-=--=-=-=- Pallionii_PA1_RUN1
>
> *** dim(data) =  554 9
> Model=MAXENT
>         Creating Maxent Temp Proj Data..
>  Runing Maxent...Unable to access jarfile 
> C:/Users/Gabri/Documents/Primule/Primula
>
>  Getting predictions...Errore in file(file, "rt") : non posso aprire 
> questa connessione
> Inoltre: Warning messages:
> 1: running command 'java -mx512m -jar 
> C:/Users/Gabri/Documents/Primule/Primula 
> allionii/Filogeografia/R1/Analisi R1/Biomod Pallionii/maxent.jar 
> environmentallayers="C:/Users/Gabri/Documents/Primule/Primula 
> allionii/Filogeografia/R1/Analisi R1/Biomod 
> Pallionii/Pallionii/MaxentTmpData/Back_swd.csv" 
> samplesfile="C:/Users/Gabri/Documents/Primule/Primula 
> allionii/Filogeografia/R1/Analisi R1/Biomod 
> Pallionii/Pallionii/MaxentTmpData/Sp_swd.csv" 
> projectionlayers="C:/Users/Gabri/Documents/Primule/Primula 
> allionii/Filogeografia/R1/Analisi R1/Biomod 
> Pallionii/Pallionii/MaxentTmpData/Pred/bio15_1_swd.csv,C:/Users/Gabri/Documents/Primule/Primula 
> allionii/Filogeografia/R1/Analisi R1/Biomod 
> Pallionii/Pallionii/MaxentTmpData/Pred/bio18_1_swd.csv,C:/Users/Gabri/Documents/Primule/Primula 
> allionii/Filogeografia/R1/Analisi R1/Biomod 
> Pallionii/Pallionii/MaxentTmpData/Pred/bio19_1_swd.csv,C:/Users/Gabri/Documents/Primule/Primula 
> allionii/Filogeografia/R1/Analisi R1/Biomod 
> Pallionii/Pallionii/MaxentTmpData/Pred [... truncated]
> 2: In file(file, "rt") :
>   cannot open file 'C:/Users/Gabri/Documents/Primule/Primula 
> allionii/Filogeografia/R1/Analisi R1/Biomod 
> Pallionii/Pallionii/models/Pallionii_PA1_RUN1_MAXENT_outputs/Pallionii_PA1_RUN1_Pred_swd.csv': 
> No such file or directory
>
> > system(command=paste("java -mx512m -jar ", 
> file.path(myBiomodOption at MAXENT$path_to_maxent.jar, "maxent.jar")))
> Unable to access jarfile C:/Users/Gabri/Documents/Primule/Primula
> Warning message:
> running command 'java -mx512m -jar 
> C:/Users/Gabri/Documents/Primule/Primula 
> allionii/Filogeografia/R1/Analisi R1/Biomod Pallionii/maxent.jar' had 
> status 1
>
>
>
>
> Il 21/11/2012 16:39, Damien Georges ha scritto:
>> Even better...
>>
>> Does the following command open MAXENT software?
>>
>> system(command=paste("java -mx512m -jar ", 
>> file.path(myBiomodOption at MAXENT$path_to_maxent.jar, "maxent.jar"))
>>
>> Best,
>>
>> Damien
>>
>>
>> On 21/11/2012 16:25, Gabriele Casazza wrote:
>>> Dear Damien,
>>> I follow your suggestions but I am not able to solve the problem.
>>> The programme write:
>>>  Creating Maxent Temp Proj Data..
>>>  Runing Maxent...Unable to access jarfile C:/Users/Gabri........
>>>
>>> Have you any other suggestions?
>>>
>>> Thank you so much
>>>
>>> Gabriele
>>>
>>>
>>>
>>> Il 21/11/2012 15:57, Damien Georges ha scritto:
>>>> Dear Gabriele,
>>>>
>>>> Did you try to play with MAXENT options? If you put maxent.jar file 
>>>> in your working directory maxent might run with default options.
>>>>
>>>> Please try the following lines of code :
>>>>
>>>> # check maxent.jar is in working directory
>>>> file.exists("maxent.jar")
>>>> # if True
>>>> myBiomodOption <- BIOMOD_ModelingOptions(MAXENT = list( 
>>>> path_to_maxent.jar = getwd()) )
>>>> # Then try to build your models with BIOMOD_modeling...
>>>>
>>>> Is it still not working?
>>>>
>>>> Hope that helps,
>>>>
>>>> Damien.
>>>>
>>>>
>>>> On 21/11/2012 14:33, Gabriele Casazza wrote:
>>>>> Dear all,
>>>>> I am not able to run maxent in the last version of Biomod2 . Even 
>>>>> if maxent.jar file is placed in the directory where I do my 
>>>>> modelling, biomod is unable to access to the file. I have not the 
>>>>> same problem using the previous version.
>>>>> Please let me know if you have any suggestions
>>>>>
>>>>> Thank you so much for all your help!  It is greatly appreciated!
>>>>> Gabriele
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Biomod-commits mailing list
>>>>> Biomod-commits at lists.r-forge.r-project.org
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits 
>>>>>
>>>>
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>>>>
>>>>
>>>
>>>
>>
>>
>
>