Github Action fail (cant find a pre-installed package)

Package development
1

Hello. I created a github action and I get this error:

Run Rscript -e 'source("auto workflow.R")'

[9](https://github.com/iamYannC/r-podcast/actions/runs/9747296399/job/26900790405#step:5:10)Error: Error in library(rvest) : there is no package called ‘rvest’

However, In my yaml file I do install rvest:

        run: Rscript -e 'install.packages(c("collapse", "rvest","stringi","tidyverse"))'

And this install job runs with no issues.
It suppose to run a auto workflow.R file that then runs the full script. Here is a link to my GitHub Repo
YAML

What do you think is the issue?
Oh and BTW feel free to clone and do some cool analysis on it! I hope to automate it, but for now I maintain a weekly update of the episodes of the R weekly podcast!

Thanks!

2

You failed to install the dependencies because system packages are missing:

install.packages() does not fail if a package fails to install, which is obviously not great.

I suggest you try GitHub - r-lib/actions: GitHub Actions for the R community with a fake DESCRITPION file that defines your dependencies. It will install the system packages (on Linux) automatically.

Alternatively, you can install the Ubuntu packages manually in the GitHub workflow.

3

Hey Gabor, thanks.
I am writing this project outside of the context of a package, and I don't have a description file.

Would you suggest using a lock file from renv to make sure my dependencies are installed instead maybe?

Or, is there a pre-made job from the r-lib which already installs system libraries?

I am not sure about the ubunto-packages. If you have a reliable reference for further reading that would also do the trick. I found various sources online regarding the whole automation process and I realise i didn't go through any official documentation or process.

Thanks again

4

You do not need to create a package. If you create a DESCRIPTION file it will serve as a lock file and you can use setup-r-dependencies to to install system packages (on Linux) and R packages.

Here is an example that is a book and not a package. The DESCRIPTION file:

and the GHA workflow:

1 Like
5

Thank you so very much for the help.
I will get on to implement (and learn....).

Regards
Yann

6

I took a diff approach and used renv. Now the failure is at something i am not sure i have to do with:
Error: Error: Error installing package 'curl':
and mainly, Package libcurl was not found in the pkg-config search path.

I really thought that one would work :
Any thought? I feel like I butchered my yml workflow by now. im really in the dark here

7

renv does not install system packages, so you'll need to install them manually. You can still use pak to look up the system packages you need. E.g.

❯ pak::pkg_sysreqs(c("rvest", "tidyverse"), sysreqs_platform = "ubuntu-22.04")
✔ Loading metadata database ... done
── Install scripts ───────────────────────────────────────────── Ubuntu 22.04 ──
apt-get -y update
apt-get -y install libcurl4-openssl-dev libssl-dev libicu-dev libxml2-dev \
  make zlib1g-dev pandoc libfreetype6-dev libjpeg-dev libpng-dev libtiff-dev \
  libfontconfig1-dev libfribidi-dev libharfbuzz-dev

── Packages and their system dependencies ──────────────────────────────────────
curl        – libcurl4-openssl-dev, libssl-dev
fs          – make
haven       – make, zlib1g-dev
knitr       – pandoc
openssl     – libssl-dev
ragg        – libfreetype6-dev, libjpeg-dev, libpng-dev, libtiff-dev
reprex      – pandoc
rmarkdown   – pandoc
sass        – make
stringi     – libicu-dev
systemfonts – libfontconfig1-dev, libfreetype6-dev
textshaping – libfreetype6-dev, libfribidi-dev, libharfbuzz-dev
xml2        – libxml2-dev