[R] system() command not working

[J Payne]

Thanks very much Roy!  I will post to R-Sig-Mac.  I browsed their archives but didn’t see anything about the issue – I might have missed something, though.  

John


On 6/4/16, 1:12 PM, "Roy Mendelssohn - NOAA Federal" <roy.mendelssohn at noaa.gov> wrote:

>Hi John:
>
>When El Capitan first came out there was a discussion in the  R-SIg-Mac  list about environmental variables not being passed down to applications  (not just R abut in general).  I believe a work around was suggested, but I would search the archives for that.
>
>So what is happening, when you run from the command line, the variables   MRT_DATA_DIR and MRTDATADIR which are defined somewhere in your environment are found in the terminal, but when the same command is run from the application they are not being found.  I would search the R-SIg-Mac archive or post to that list, because i can’t remember what the work around was for it.
>
>HTH,
>
>-Roy
>
>> On Jun 4, 2016, at 11:59 AM, J Payne <jcpayne at uw.edu> wrote:
>> 
>> 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]]
>> 
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>
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>**********************
>Roy Mendelssohn
>Supervisory Operations Research Analyst
>NOAA/NMFS
>Environmental Research Division
>Southwest Fisheries Science Center
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>