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actions's Issues

configuring custom environment variables for the check

Hi,

first of all - this is amazing. Works like a charm!

However, I cant wrap my head around how to configure the action to account for additional environment variables I want to set for the test, e.g. _R_CHECK_THINGS_IN_OTHER_DIRS_

If I see correctly, these get parsed here on line 122. But I am not sure on which machine they have to be set (e.g. in the virtual machine) and how I can customize these.

I am sorry if this is trivial, I would be happy, if you could point me in a direction. If it is not trivial, than it also is not very urgent and the issue can be closed.

Thank you!

Checkout submodules by default?

Loving the new Github actions approach to rhub! One request, could the r-hub/actions/checkout@v1 action checkout submodules by default? Or have an option to enable?

Thanks!

pak-builder action

Prototype working on macOS. Will keep this issue until all three platforms work property.

General

  • Automatically select between dev and stable repo
  • Remove older version, from the history as well, because the repo will get huge very quickly otherwise.
  • Add a check, to make sure that the built package works.
  • Need a GH API token.

macOS

  • macOS
  • macOS: do not hardcode versions of libcurl and its dependencies
  • macOS: fix 3.3
  • macOS: fix 'devel'

Windows

  • Windows

Linux

  • Linux
  • Fix Dockerfile on R 3.3

Checking on windows with `configure.ac` script will always result in error due to CRLF issues

Even though I already made sure that I submitted the configure.ac with LF only line endings (by git ls-files --eol, see attached image) this will still be converted due to incorrect configuration within the git's checking process and result in R CMD check warnings which will lead to error.
 
image

See my repository job: https://github.com/caiohamamura/gdalBindings-r/actions/runs/9275022762/job/25518759238. Every other machines are passing gracefully.

Installing package cachem causes an error in the action for "atlas", but not in a bare container

This error reproduces consistently in my github action, but not in a bare container.

Snippet of error in github action: https://github.com/bertcarnell/lhs/actions/runs/9147268987/job/25148473610

ℹ Building fastmap 1.2.0
  ℹ Building xfun 0.44
  ✔ Built fastmap 1.2.0 (3.1s)
  ✔ Installed fastmap 1.2.0  (1s)
  ℹ Building cachem 1.1.0
  ✖ Failed to build cachem 1.1.0 (573ms)
  Error: 
  ! error in pak subprocess
  Caused by error in `stop_task_build(state, worker)`:
  ! Failed to build source package cachem.
  Full installation output:
  * installing *source* package ‘cachem’ ...
  ** package ‘cachem’ successfully unpacked and MD5 sums checked
  staged installation is only possible with locking
  ** using non-staged installation
  ** libs
  using C compiler: ‘gcc (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)’
  gcc -I"/opt/R/devel-gcc/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -Wall -pedantic -c cache.c -o cache.o
  gcc -I"/opt/R/devel-gcc/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -Wall -pedantic -c init.c -o init.o
  gcc -shared -L/opt/R/devel-gcc/lib/R/lib -L/usr/local/lib -o cachem.so cache.o init.o -L/opt/R/devel-gcc/lib/R/lib -lR
  installing to /tmp/RtmpDWvXgn/pkg-lib23d119c413e/cachem/libs
  ** R
  ** byte-compile and prepare package for lazy loading
  Error in dyn.load(file, DLLpath = DLLpath, ...) : 
    unable to load shared object '/github/home/R/x86_64-pc-linux-gnu-library/4.5/rlang/libs/rlang.so':
    libsvml.so: cannot open shared object file: No such file or directory
  Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
  Execution halted
  ERROR: lazy loading failed for package ‘cachem’
  * removing ‘/tmp/RtmpDWvXgn/pkg-lib23d119c413e/cachem’
  ---
  Backtrace:
  1. pak::lockfile_install(".github/pkg.lock")
  2. pak:::remote(function(...) { …
  3. err$throw(res$error)

Attempt to reproduce the error in a bare container, outside of github actions, but this was successful

docker pull ghcr.io/r-hub/containers/atlas:latest
sudo docker run -ti --rm -v /mnt/c/repositories:/home/docker -w /home/docker -u root --name atlas_interactive ghcr.io/r-hub/containers/atlas

yum update -y
yum install -y gmp-devel pandoc texlive
R
install.packages(c("knitr", "rmarkdown", "Rcpp", "testthat", "DoE.base"))
install.packages(c("cachem"))
q()
R CMD build lhs
R CMD check lhs_*.tar.gz

macOS pak build does not work on High Sierra any more

> pak::pkg_install("usethis")
Error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/pak/library/curl/libs/curl.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/pak/library/curl/libs/curl.so, 6): Symbol not found: ____chkstk_darwin
  Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pak/library/curl/libs/curl.so
  Expected in: /usr/lib/libSystem.B.dylib
 in /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pak/library/curl/libs/curl.so
Type .Last.error.trace to see where the error occurred

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