Cambie mi sintaxis de entrada a:
input<-list.files(path=".",".hdf",all.files=T,recursive=T)

y ahora mi error es:

> reprojectHDF(hdfName=input,filename=outname,MRTpath="~/MRT/bin",+ resample_type="NEAREST_NEIGHBOR",+ proj_type="GEO",datum='WGS84')******************************************************************************

MODIS Reprojection Tool (v4.1 March 2009)
Start Time:  Tue Jul 29 01:37:37 2014

------------------------------------------------------------------

Warning: gctp_call : Environmental Variable Not Found
     : MRT_DATA_DIR nor MRTDATADIR not defined
Error: GetInputGeoCorner : General Processing
     : Error converting input projection coordinates to lat/long coordinates.
Fatal Error, Terminating...
[1] FALSE



2014-07-29 1:24 GMT-05:00 A. Robles R. <albert.physik@gmail.com>:

> Saludos, estoy intentando usar la función reprojectHDF() (
> http://r-gis.net/?q=ModisDownload).
>
> ####
> source('ModisDownload.R')
> library(raster)
> library(RCurl)
> path<-"~/R/MODIS/Data/Test"
> input<-list.files(path,"*.hdf",all.files=T,recursive=T,full.names=T)
> input
> outname<-paste(substr(input[1],40,45),".tif",sep='')
> outname
> reprojectHDF(hdfName=input,filename=outname,MRTpath="~/MRT/bin",
> resample_type="NEAREST_NEIGHBOR",
> proj_type="GEO",datum='WGS84')
> ####
> Pero me resulta el siguiente mensaje de error:
> ####
> > reprojectHDF(hdfName=input,filename=outname,MRTpath="~/MRT/bin",
> + resample_type="NEAREST_NEIGHBOR",
> + proj_type="GEO",datum='WGS84')
>
> ******************************************************************************
> MODIS Reprojection Tool (v4.1 March 2009)
> Start Time: Tue Jul 29 00:57:18 2014
> ------------------------------------------------------------------
> Error: ReadHDFHeader : Opening Input Header File
> : Unable to open
> /home/rral/R/MODIS/Data/Test//home/rral/R/MODIS/Data/Test/MOD13Q1.A2000065.h09v08.005.2008238073751.hdf
> Fatal Error, Terminating...
> [1] FALSE
> ####
> Toda sugerencia es bienvenida.
> ####
> PD: mis variables de entrada son:
> > input
> [1]
> "/home/rral/R/MODIS/Data/Test/MOD13Q1.A2000065.h09v08.005.2008238073751.hdf"
> [2]
> "/home/rral/R/MODIS/Data/Test/MOD13Q1.A2000065.h09v09.005.2008238081536.hdf"
> [3]
> "/home/rral/R/MODIS/Data/Test/MOD13Q1.A2000065.h10v08.005.2008238053313.hdf"
> [4]
> "/home/rral/R/MODIS/Data/Test/MOD13Q1.A2000065.h10v09.005.2008238061408.hdf"
> y
> > outname
> [1] "2000065.tif
>
> --
> *Atte:*   *A. Robles R.*
>



-- 
*Atte:*   *A. Robles R.*

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