[R] system() command not working

[Berend Hasselman]

> On 4 Jun 2016, at 22:12, 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.
> 

I can't find the discussion on R-SIG-Mac list. But you can try this:

MRT_DATA_DIR=<whatever> open -a Rstudio

or  

MRT_DATA_DIR=<whatever> open -a R

Try it and see what happens.
It may even be possible to put something in .Rprofile  setting your environment variables.

Berend Hasselman

> 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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> 
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> 
> ______________________________________________
> R-help at 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.