Hi, Ah, of course - the wrapper would be a shell wrapper not an R wrapper ...
### #!/bin/sh cd /path/to/project Rscript /path/to/script.R /path/to/config_file ### Thanks so much! Ben On Tue, Apr 14, 2020 at 2:13 PM Thierry Onkelinx <thierry.onkel...@inbo.be> wrote: > Dear Ben, > > I think that you first need to go to your project and then start Rscript > from that location. renv() needs to pick up the .Renviron file located at > the root of your project. > > Best regards, > > ir. Thierry Onkelinx > Statisticus / Statistician > > Vlaamse Overheid / Government of Flanders > INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND > FOREST > Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance > thierry.onkel...@inbo.be > Havenlaan 88 bus 73, 1000 Brussel > www.inbo.be > > > /////////////////////////////////////////////////////////////////////////////////////////// > To call in the statistician after the experiment is done may be no more > than asking him to perform a post-mortem examination: he may be able to say > what the experiment died of. ~ Sir Ronald Aylmer Fisher > The plural of anecdote is not data. ~ Roger Brinner > The combination of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body of data. > ~ John Tukey > > /////////////////////////////////////////////////////////////////////////////////////////// > > <https://www.inbo.be> > > > Op di 14 apr. 2020 om 19:53 schreef Ben Tupper <btup...@bigelow.org>: > >> Whoops! The silly "send" button jumped out and grabbed my cursor before I >> was ready for it. Second try... >> >> I am using renv (https://rstudio.github.io/renv/) to maintain a project >> environment in a directory (ala '/path/to/project'). >> >> Within the project I have a number of scripts that I call with one >> argument >> using... >> >> $ Rscript /path/to/script.R /path/to/config_file >> >> I can kick this off successfully with the renv environment when I manually >> start Rscript within the project directory. Now I would like to be able to >> hand the script kick-off to either crontab or the PBS queueing system. >> But >> I haven't figured out how to get the instance of R that is kicked off to >> do >> so using the renv project space (i.e. using the R libraries as established >> in the project.) >> >> At first I thought I would call a simple wrapper script such that accepted >> two arguments '/path/to/script.R' and '/path/to/config_file'. I planned to >> use ... >> >> ### >> args <- commandArgs(trailingOnly = TRUE) >> path_to_script <- args[1] >> path_to_config <- args[2] >> renv::run(path_to_script, >> project = '/path/to/project') >> ### >> >> Unfortunately renv::run() doesn't provide a vehicle for passing other >> script arguments along. So, in this case, there's no way to communicate >> the configuration file to the script. >> >> Is there a recommended way to call Rscript such that the renv environment >> gets picked up? >> >> Thanks! >> Ben >> >> >> On Tue, Apr 14, 2020 at 1:41 PM Ben Tupper <btup...@bigelow.org> wrote: >> >> > Hi, >> > >> > I am using renv (https://rstudio.github.io/renv/) to maintain a project >> > environment in a directory (ala /path/to/project) >> > >> > >> > Within the project I have a number of scripts that I call using... >> > >> > $ Rscript /path/to/script.R /path/to/config_file >> > >> > I can kick this off successfully with the renv environment when I >> manually >> > start Rscript within the project directory. Now I would like to be able >> to >> > hand the script kick off to either crontab or the PBS queueing system. >> > >> > At first I thought I would actually call a wrapper script such that >> > accepted two arguments '/path/to/script.R' and '/path/to/config_file'. I >> > planned to use >> > >> > renv::run('/path/to/script.R', >> > >> > >> > -- >> > Ben Tupper >> > Bigelow Laboratory for Ocean Science >> > East Boothbay, Maine >> > http://www.bigelow.org/ >> > https://eco.bigelow.org >> > >> > >> >> -- >> Ben Tupper >> Bigelow Laboratory for Ocean Science >> East Boothbay, Maine >> http://www.bigelow.org/ >> https://eco.bigelow.org >> >> [[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. >> > -- Ben Tupper Bigelow Laboratory for Ocean Science East Boothbay, Maine http://www.bigelow.org/ https://eco.bigelow.org [[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.
