Github Actions - R package R-CMD-Check "PhantomJS not found" - r

Question

I am using GitHub actions for CI of my R package. I am trying using both testthat and shinytest in my package. I have the package structure set up correctly according to the shinytest documentation. When I run R-CMD-CHECK in RStudio, my package (including both testthat and shinytest testing works).
My GitHub Actions .yaml workflow is:
on:
push:
branches:
- main
- master
pull_request:
branches:
- main
- master
name: R-CMD-check
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: false
matrix:
config:
- {os: windows-latest, r: 'release'}
- {os: macOS-latest, r: 'release'}
- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
steps:
- uses: actions/checkout#v2
- uses: r-lib/actions/setup-r#v1
with:
r-version: ${{ matrix.config.r }}
- uses: r-lib/actions/setup-pandoc#v1
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache#v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
- name: Install system dependencies
if: runner.os == 'Linux'
run: |
while read -r cmd
do
eval sudo $cmd
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}
- name: Check
env:
_R_CHECK_CRAN_INCOMING_REMOTE_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
shell: Rscript {0}
- name: Upload check results
if: failure()
uses: actions/upload-artifact#main
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
When I commit to the repository, the check fails on Windows and Mac OS but works on Ubuntu.
The error that I am I am getting on both Windows and Mac OS is:
> test_check("mypackage")
-- 1. Error: application works (#test-appdir.R#6) -----------------------------
PhantomJS not found.
I don't think this is a problem with my package or tests. I think there is something misconfigured about my .yaml. How can I resolve this issue with PhantomJS in my workflow?

Answer 1

The easy solution will be to go to the project where there is used PhantomJS and the Github Actions is turned on. We will go to shiny project and precisely to:
https://github.com/rstudio/shiny/blob/master/.github/workflows/R-CMD-check.yaml
We could find out there that:
- name: Install system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
sudo -s eval "$sysreqs"
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}
- name: Find PhantomJS path
id: phantomjs
run: |
echo "::set-output name=path::$(Rscript -e 'cat(shinytest:::phantom_paths()[[1]])')"
- name: Cache PhantomJS
uses: actions/cache#v1
with:
path: ${{ steps.phantomjs.outputs.path }}
key: ${{ runner.os }}-phantomjs
restore-keys: ${{ runner.os }}-phantomjs
- name: Install PhantomJS
run: >
Rscript
-e "if (!shinytest::dependenciesInstalled()) shinytest::installDependencies()"
We easily could check that there is separate chunk of code only to be sure that PhantomJS localization is known or if it should be installed.
You could paste this part of code to your yaml file. However the best way might to be follow the pipeline of shiny project,

Answer 2

It's hard to investigate the issue without detailed logs and no information about what dependencies (remotes) are being installed in Query dependencies step. It seems the PhantomJS dependency is not being installed at all. The workflow succeeds on ubuntu-20.04 because the runner has PhantomJS installed out-of-the-box. You can see all the installed software on provided runner types here. The other runner types used in the workflow above (windows-latest and macOS-latest) are missing PhantomJS. That's why your workflow fails on Windows and MacOS but succeeds on Ubuntu.