[R] system() command not working

[J Payne]

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!  

 

 

 


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