system() command not working

Thanks Berend, that?s super useful.  In summary, here is what I found:

The problem (if I understand correctly) is that R was not passing environment variables to OSX El Capitan successfully.  In any case:

These do not work:
1. Setting the environment variable in my .bash_profile (for example ?MTR_DATA_DIR="/Applications/MRT/data"); or 
2. Adding the same environment variable to .Rprofile in my home directory.

These do work (hooray!):
3. Changing the environment variable using Sys.setenv(MRT_DATA_DIR="/Applications/MRT/data") inside R at the R command line; or
4. Typing ?MRT_DATA_DIR="/Applications/MRT/data" open -a Rstudio? in the Terminal.  This latter method is an effective workaround and wonderful to have in my bag of tricks, but is slightly clumsier since I have to remember to open RStudio this way  each time.  

I?m very grateful to you and Roy for your help.

John

On 6/5/16, 3:28 AM, "Berend Hasselman" <bhh at xs4all.nl> wrote:

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!  








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