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" <jcpa...@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" <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.
