Thanks very much Roy! I will post to R-Sig-Mac. I browsed their archives but didn’t see anything about the issue – I might have missed something, though.
John On 6/4/16, 1:12 PM, "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. > >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.
