[R] Package renv and Rscript

[Ben Tupper]

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.onkelinx using 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.onkelinx using inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be
>
>
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>
>
> Op di 14 apr. 2020 om 19:53 schreef Ben Tupper <btupper using 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 <btupper using 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]]
>>
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>>
>

-- 
Ben Tupper
Bigelow Laboratory for Ocean Science
East Boothbay, Maine
http://www.bigelow.org/
https://eco.bigelow.org

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