[Biomod-commits] Maxent probelm

[Gabriele Casazza]

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 
>>>>
>>>
>>> _______________________________________________
>>> 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 
>>>
>>>
>>
>>
>
>


-- 
Gabriele Casazza
Università di Genova
DISTAV
Corso Dogali 1M
I - 16136 GENOVA (Italy)
-----------------------------
Tel: +39 010 2099361
Fax:+39  010 2099377
Email:  gabriele.casazza at unige.it
www.polobotanicohanbury.it


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