[R-sig-Geo] connection error when calling maxent()

[Rafael Wüest]

Dear Robert,

Unfortunately, the problem is not completely solved for me yet. I am trying to run maxent() on a cluster, because I'm modeling >200 species, using 8 different parameterizations and 4 modeling algorithms (maxent is one of them), which results in >6000 models. The cluster is running R 2.12.2 and I can't update it on my own.

As a workaround, I tried to specify the path option in the maxent() function because I suspected some process might interfere with the temporary Raster directory. This seemed to run for quite some time, but after maxent being called for the 46th on one of the cluster's CPU, it crashed with the same error

> Error: No features available: select more feature types or deselect auto features
> Error in file(con, "r") : cannot open the connection
> Calls: run4models ... maxent -> maxent -> .local -> unlist -> readLines -> file
> In addition: Warning message:
> In file(con, "r") :
>   cannot open file '/.../me_output/xval/species.lambdas': No such file or directory
> Execution halted

Do you have any idea how I could still make maxent() functional using R 2.12.2?

Rafael


On 12.01.2012, at 01:33, Robert J. Hijmans wrote:

> Rafael,
> 
> Please send more info about what you are doing. It appears that the MaxEnt output file gets overwritten by another process. Can you also send your sessionInfo() (after first updating R to a more recent version)?
> 
> Robert
> 
> 
> On Wed, Jan 4, 2012 at 8:52 AM, rafael.wueest <rafael.wueest at wsl.ch> wrote:
> Hi Folks
> 
> when I am trying to call the maxent() function within a function I created,
> I am getting the following error:
> 
> Error in file(con, "r") : cannot open the connection
> In addition: Warning message:
> In file(con, "r") :
>  cannot open file
> '/var/folders/ft/fthJYD+6GkCvmcCArZBaQU++waU/-Tmp-/R_raster_tmp/maxent/10943312360/species.lambdas':
> No such file or directory
> 
> I am here also pasting some output of
> >traceback()
> 7: file(con, "r")
> 6: readLines(paste(dirout, "/species.lambdas", sep = ""))
> 5: unlist(readLines(paste(dirout, "/species.lambdas", sep = "")))
> 4: .local(x, p, ...)
> 3: maxent(background, occ, args = me.args) at run4models_restios.r#558
> ...
> 
> I am using JGR on a Mac and downloaded the newest dismo (CRAN sources) and
> maxent version (see below).
> 
> Can anyone help me? I am happy to provide more detailed information...
> 
> Rafa
> 
> >maxent()
> This is MaxEnt version 3.3.3k
> 
> >sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods
> [8] base
> 
> other attached packages:
>  [1] gbm_1.6-3.1           survival_2.36-5       gam_1.04.1
>  [4] PresenceAbsence_1.1.5 maptools_0.8-10       lattice_0.19-33
>  [7] foreign_0.8-42        rgdal_0.6-33          dismo_0.7-14
> [10] raster_1.9-13         sp_0.9-84             JGR_1.7-7
> [13] iplots_1.1-4          JavaGD_0.5-4          rJava_0.9-1
> 
> loaded via a namespace (and not attached):
> [1] grid_2.12.2  tools_2.12.2
> Warning message:
> 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
> 
> 
> --
> View this message in context: http://r-sig-geo.2731867.n2.nabble.com/connection-error-when-calling-maxent-tp7151125p7151125.html
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> 
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--
Rafael Wüest
Swiss Federal Research Institute WSL
Zürcherstrasse 111
8903 Birmensdorf
Switzerland

+41 44 7392126
rafael.wueest at wsl.ch
http://www.wsl.ch/info/mitarbeitende/wueest