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" <b...@xs4all.nl> wrote: > >> On 4 Jun 2016, at 22:12, Roy Mendelssohn - NOAA Federal >> <roy.mendelss...@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 <jcpa...@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@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.mendelss...@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@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. > ______________________________________________ R-help@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.