Hi Aseem,
I ran into this problem some time ago and posted my solution to the
r-sig-geo list. This was on a Linux server. I'm not sure what the default
upper file limit is on windows, but this may give you some clues. Also, I
saw several other posts and responses with the same problem, I've pasted a
link to one of those threads below.

HTH,

Zack

# my solution
http://r-sig-geo.2731867.n2.nabble.com/solved-raster-ncdf4-error-too-many-open-files-td7583723.html

#  a similar post
http://r-sig-geo.2731867.n2.nabble.com/raster-rgdal-problem-Too-many-open-files-Linux-td7584338.html


On Tue, Mar 11, 2014 at 10:27 AM, Aseem Sharma <nature.aseem@gmail.com>wrote:

> hi,
> i have big netCDF file that archive daily climate data since 1950-01-01 to
> 2010-12-31. I want to extract this CDF file so that new will have same data
> only starting from 1980-01-01 ( i e recent 30 years only).
> I tried with subset function of raster package. after overnight running,
> it gives me error of too many files.
>
> So how can i extract  only recent years netCDF.
>
> My code so far:
>  subset(data,10592:22280, drop=TRUE,filename="data_19800101_20101231.nc
> ",overwrite=TRUE)
>
>  where
> data is my netCDF with data from 1950-01-01 and 10592:22280 is the no of
> days between 1980-01-01 to 2010-12-31.
>
> Error ( after more than 12 hours running )
>
> Error in R_nc_open: Too many open files
> Error in open.ncdf(x@file@name) :
>   Error in open.ncdf trying to open file Z:\Thesis\Data\CCC
> Data\Tmn_19500101_20101231.nc
>
> Traceback after error
> > traceback()
> 13: stop(paste("Error in open.ncdf trying to open file", con))
> 12: open.ncdf(x@file@name)
> 11: .openConnection(x, ...)
> 10: readStart(x@layers[[i]], con.check = 103, ...)
> 9: readStart(x@layers[[i]], con.check = 103, ...)
> 8: readStart(x, ...)
> 7: readStart(x, ...)
> 6: .local(x, filename, ...)
> 5: writeRaster(x, filename, ...)
> 4: writeRaster(x, filename, ...)
> 3: .local(x, ...)
> 2: subset(Tmin, 10592:22280, drop = TRUE, filename =
> "Tmn_19800101_20101231.nc",
>        overwrite = TRUE)
>
> Session info
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>  [1] zyp_0.10-1          Kendall_2.2         scales_0.2.3        plyr_1.8
>          ggplot2_0.9.3.1
>  [6] reshape2_1.2.2      zoo_1.7-10          rasterVis_0.27
>  hexbin_1.26.3       latticeExtra_0.6-26
> [11] RColorBrewer_1.0-5  lattice_0.20-23     ncdf_1.6.6
>  raster_2.2-12       sp_1.0-14
>
> loaded via a namespace (and not attached):
>  [1] boot_1.3-9       colorspace_1.2-4 dichromat_2.0-0  digest_0.6.4
> gtable_0.1.2
>  [6] labeling_0.2     MASS_7.3-29      munsell_0.4.2    proto_0.3-10
> stringr_0.6.2
> [11] tools_3.0.2
> >
> I couldn't attache the exact data. One smaller version of same data is
> here<https://www.dropbox.com/s/yx9q09iek593f81/obs1.nc>
> .
>
> Thank you,
> a
>
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>
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