[R] system() command not working

Sun Jun 5 22:17:55 CEST 2016

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!  
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 	[[alternative HTML version deleted]]
>>> 
>>> ______________________________________________
>>> 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.
>> 
>> **********************
>> "The contents of this message do not reflect any position of the U.S. Government or NOAA."
>> **********************
>> Roy Mendelssohn
>> Supervisory Operations Research Analyst
>> NOAA/NMFS
>> Environmental Research Division
>> Southwest Fisheries Science Center
>> ***Note new address and phone***
>> 110 Shaffer Road
>> Santa Cruz, CA 95060
>> Phone: (831)-420-3666
>> Fax: (831) 420-3980
>> e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
>> 
>> "Old age and treachery will overcome youth and skill."
>> "From those who have been given much, much will be expected" 
>> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>> 
>> ______________________________________________
>> 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.
>