I’ve posted this question on StackExchange at http://stackoverflow.com/questions/37604466/r-system-not-working-with-modis-reprojection-tool, but haven’t received any replies. I’m hoping that someone who understands the operation of the R system() command can help.
I have a command that works when typed into the Terminal on a Mac (OSX El Cap), but exactly the same command fails when called from R using `system()`. I am trying to batch-process MODIS satellite files using a small program called the MODIS Reprojection Tool (https://lpdaac.usgs.gov/tools/modis_reprojection_tool). My software is all up to date. This is a simple example in which I mosaic two files. The names of the two files are in a text input file called `input.list`. The command just tells the `mrtmosaic` routine where to find the input list and where to put the output. This command works correctly in the Terminal: /Applications/Modis_Reprojection_Tool/bin/mrtmosaic -i ~/temp/input.list -o ~/temp/output.hdf However, if I put exactly the same string into a variable and run it from R (using RStudio), it fails: comstring<-"/Applications/Modis_Reprojection_Tool/bin/mrtmosaic -i ~/temp/input.list -o ~/temp/output.hdf" system(comstring) >Warning: gctp_call : Environmental Variable Not Found: MRT_DATA_DIR nor MRTDATADIR not defined Error: GetInputGeoCornerMosaic : General Processing Error converting lat/long coordinates to input projection coordinates. Fatal Error, Terminating... The strange thing is that the system knows what the environment variables are. In the terminal, the command `echo $MRT_DATA_DIR` shows the correct directory: /Applications/Modis_Reprojection_Tool/data I don't see why it would have trouble finding the variables from an `R system()` call when it has no trouble in the Terminal. I'm very stumped! [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
