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License: MIT License
GitHub Actions for R-hub
License: MIT License
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!
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!
Just to wanted to check if this is expected/intended behaviour - when the clang-asan
container detects undefined behaviour, the workflow still reports a successful completion. Should the workflow fail on detection, or is the intent to always inspect the output results? Thanks!
Can be seen in this run: https://github.com/andrjohns/QuickJSR/actions/runs/9077288982/job/24941850497
Dear all, I am using the "check-standard"
setup to run R-CMD-check on a package with Fortran code, and the check fails for macOS-latest. At first glance, it seems to me that the Fortran compiler is not in place. Is this an error on my part, a bug, or a known limitation?
Here is the failing test: https://github.com/cjvanlissa/bain/runs/1828646234?check_suite_focus=true
On windows R reports
files 'DESCRIPTION', 'Meta/package.rds' have the wrong MD5 checksums
Prototype working on macOS. Will keep this issue until all three platforms work property.
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.
See my repository job: https://github.com/caiohamamura/gdalBindings-r/actions/runs/9275022762/job/25518759238. Every other machines are passing gracefully.
Maybe this is an RCurl bug, but I figured I'd start here. rhub_check("https://github.com/Meredith-Lab/volcalc/", platforms = "windows", branch = "master")
is failing because of an error building RCurl
: https://github.com/Meredith-Lab/volcalc/actions/runs/9023334902/job/24794891961
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
> 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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