Rafael,

The issue here would be the version of raster, not R (as long as it is >=
2.11.0); but I agree that you have found a good solution.  And the error is
a rather different one that you originally reported:

> Error: No features available: select more feature types or deselect auto
features

Unless you did not copy this line when you first reported the problem...

That error comes from MaxEnt, and clearly states that there is something
wrong with the feature selection. I do not know why. Perhaps because of one
of the MaxEnt options you use, perhaps in combination with only a few point
records? That is a subject more suitable for the MaxEnt discussion forum.

Because MaxEnt fails to run, further errors occur, but the trouble starts
with the line above. So it seems that your method works, except for MaxEnt
run 46

Robert


On Sat, Jan 14, 2012 at 3:51 AM, Rafael Wüest <rafael.wueest@wsl.ch> wrote:

> 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@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
> > Sent from the R-sig-geo mailing list archive at Nabble.com.
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
>
>
>
> --
> Rafael Wüest
> Swiss Federal Research Institute WSL
> Zürcherstrasse 111
> 8903 Birmensdorf
> Switzerland
>
> +41 44 7392126
> rafael.wueest@wsl.ch
> http://www.wsl.ch/info/mitarbeitende/wueest
>
>
>
>

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