[R] system() command not working

Sun Jun 5 22:51:41 CEST 2016

I forgot to add that setting the environment variable in .Renviron in my home directory *also* works.  I have updated my question on Stackoverflow to include these answers.

John

On 6/5/16, 1:17 PM, "J Payne" <jcpayne at uw.edu> wrote:

>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]]
>>>> 
>>>> ______________________________________________
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>>>> 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.
>>