using system packages

[da5nsy]

Forgive the noob questions (I'm new to both R and apptainer...)

I'm trying to add a dependency to this container.
I modified install.R:

options(repos = c(
  carpentries = "https://carpentries.r-universe.dev/", 
  CRAN = "https://cran.rstudio.com/"
))

renv::install('ggplot2')
renv::install("WEHI-Education/CarpentriesSlides")

and then ran ./contain-R.sif R.

It failed (I'll attach full log), I think because it's not using or installing several system packages:

x Missing 14 system packages. You'll probably need to install them manually:
+ git                 - credentials, gitcreds         
+ libfontconfig1-dev  - systemfonts                   
+ libfreetype6-dev    - ragg, systemfonts, textshaping
+ libfribidi-dev      - textshaping                   
+ libgit2-dev         - gert                          
+ libharfbuzz-dev     - textshaping                   
+ libjpeg-dev         - ragg                          
+ libpng-dev          - ragg                          
+ libssl-dev          - curl, openssl                 
+ libtiff-dev         - ragg                          
+ libx11-dev          - clipr                         
+ libxml2-dev         - xml2                          
+ libxslt-dev         - xslt                          
+ pandoc              - knitr, pkgdown, rmarkdown 

Any tips on how to resolve this?

[da5nsy]

This was resolved by running ./contain-R.sif R as sudo.

[bast]

It should not be necessary to run as sudo. I will have a look and try to reproduce it.

[da5nsy]

It might be to do with how I have R installed locally. I found yesterday that I needed to run it as sudo in order to install any new R packages, which does not sound like the way things are meant to work 😬