GitHub actions fix: r-cmd-check

[evaham1]

Issue:

Github actions have been failing on scheduled weekly triggers and everytime a branch is pulled or PRs made for the last few months.

Changes to github actions:

Refactored the code in github actions to ensure tests run properly across macOS, windows and linux github runners:

• Uncommented the windows and macOS matrix configurations so tests run on all three operating systems
• Install system dependencies step changed because r-hub/sysreqs doesn’t work anymore:
  • The GitHub repo for sysreqs was archived on 15th April 2024 (https://github.com/r-hub/sysreqs), plus the server which sysreqs needs to access isn't avaliable (sysreqs.r-hub.io). This caused an error when sysreqs was triggered in the GitHub action SSL peer certificate or SSH remote key was not OK
• Installing things without using sysreqs:
  • First used GitHub action to install system and package dependencies r-lib/actions/setup-r-dependencies@v2
  • Then there were still some additional dependences missing so:
    • Install xquartz and gcc for macOS (NB also had to do this locally when working on a mac)
    • Install pandoc and qpdf for linux
• R CMD check: changed rmcdcheck to devtools::check() because the former was failing on windows runner
  • Basically on windows the issue seemed to be during vignette building when parallelisation was used workers couldn’t access mixOmics functions. This was probably due to fact that windows (unlike Mac and linux) can’t do FORK clusters so workers do not share memory/workspaces, so somehow not all the functions can be accessed. This was fixed by running devtools::install() and then devtools::check, so for this reason we have swapped from rmdcheck to devtools to perform the check. Check should still be performed in the same way.
  • Params have been kept the same for the normal r-cmd-check:
    • rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
    • devtools::check(args = c("--no-manual"), error_on = "warning", check_dir = "check")
  • Params have been kept the same for the cran r-cmd-check check:
    • rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--ignore-vignettes", "--run-dontrun"), error_on = "never", check_dir = "check/asCRAN", build_args = c("--no-build-vignettes"))
    • options(devtools.check.dir = "check/asCRAN", devtools.check.warning = "never") devtools::check(args = c("--no-manual", "--as-cran", "--ignore-vignettes", "--run-dontrun"), build_args = c("--no-build-vignettes"))
• Commented out notify slack because it didn’t work

Additional changes

As well as the github changes, changes to update dependencies to latest R version and new tensor methods were performed by Brendan Lu see:
#313
#314
#315