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. > [[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.
