run-rchk action cannot load libR.so

[ms609]

Describe the bug run-rchk cannot load libR.so

To Reproduce I have a GitHub action script including the Basic configuration given at the actions/run-rchk readme:

jobs:  
  rchk:
    runs-on: ubuntu-latest
    container:
      image: rhub/ubuntu-rchk
      options: --user=root
    steps:
    - uses: actions/checkout@v2
    - uses: r-lib/actions/run-rchk@v2

The run fails with

 Error in dyn.load(dll_file) : 
    unable to load shared object '/tmp/RtmpWikvGF/file1935703f34e/glue/libs//glue.so':
    libR.so: cannot open shared object file: No such file or directory
  Calls: <Anonymous> ... load_private_packages -> load_private_package -> dyn.load
  Execution halted

[randy3k]

I think it is because setup-r-dependencies@v2 not working with the docker image rhub/ubuntu-rchk. Try the following instead?

  rchk:
    runs-on: ubuntu-latest
    container:
      image: rhub/ubuntu-rchk
      options: --user=root
    steps:
    - uses: actions/checkout@v2
    - uses: r-lib/actions/run-rchk@v2
      with:
        setup-only: true
    - uses: r-lib/actions/setup-r-dependencies@v1
      with:
        cache-version: rchk-1
    - uses: r-lib/actions/run-rchk@v2
      with:
        run-only: true

[ms609]

Thanks for the suggestion; however, I still see the error in the setup-r-dependencies@v1 step.

 Error in dyn.load(dll_file) : 
    unable to load shared object '/tmp/RtmpldVcb7/file18c1d8a9878/glue/libs//glue.so':
    libR.so: cannot open shared object file: No such file or directory
  Calls: saveRDS ... load_private_packages -> load_private_package -> dyn.load
  Execution halted

[randy3k]

trying URL 'r-lib.github.io/p/pak/stable/src/contrib/pak_0.2.0.9000_R4-2_x86_64-pc-linux-musl.tar.gz'

It seems the pak binary from r-lib.github.io is not working with the docker rhub/ubuntu-rchk. A solution is to change the repo to CRAN so that we install it from source

install.packages("pak", repos = "https://cran.rstudio.com/")

However, it will take a few minutes to install.

[ms609]

Thanks, I added a step

    - name: Install `pak` from source
      run: |
        install.packages("pak", repos = "https://cran.rstudio.com/")
      shell: Rscript {0}

which installs pak successfully, but r-lib/actions/setup-r-dependencies@v1 still attempts to install pak, meeting the same failure point. Run log

[randy3k]

Ya, you need to fork this repo and change this line to

install.packages("pak", repos = "https://cran.rstudio.com/")

I figured out that the binary of pak shipped from r-lib.github.io/p/pak requires the shared library libR.so. But unfortunately, the image rhub/ubuntu-rchk only has libR.a. So the current workaround is to install pak from source.

There are a few viable solutions to resolve the issue.

1. Request rhub/ubuntu-rchk to build R with flag --enable-R-shlib
2. Fork rhub/ubuntu-rchk and build another image which build R with flag --enable-R-shlib
3. Build another image on top of rhub/ubuntu-rchk that comes with pak.

@gaborcsardi what do you think?

[randy3k]

@ms609

Forgot to mention that another solution is to completely skip setup-r-dependencies like this,

  rchk:
    runs-on: ubuntu-latest
    container:
      image: rhub/ubuntu-rchk
      options: --user=root
    steps:
    - uses: actions/checkout@v2
    - uses: r-lib/actions/run-rchk@v2
      with:
        setup-only: true
    - name: Install package
      run: |
		install.packages('remotes', repos = "https://cran.rstudio.com/")
        remotes::install_local()
      shell: Rscript {0}
    - uses: r-lib/actions/run-rchk@v2
      with:
        run-only: true

But it also means that your package's dependencies would be built every time. If you still want the ability to cache dependencies, you would refer to this retired action that based on remotes.

Update:

I have put together a version of setup-r-dependencies that works with rhub/ubuntu-rchk.

Example:

  rchk:
    runs-on: ubuntu-latest
    container:
      image: rhub/ubuntu-rchk
      options: --user=root
    steps:
    - uses: actions/checkout@v2
    - uses: r-lib/actions/run-rchk@v2
      with:
        setup-only: true
    - uses: randy3k/gh-actions/r-install-deps@main
      with:
        cache-version: rchk-1
    - name: Install package
      run: |
        remotes::install_local()
      shell: Rscript {0}
    - uses: r-lib/actions/run-rchk@v2
      with:
        run-only: true

[ms609]

Thanks – your update fix seems to have rchk up and running on the github action!

Thanks for your help with this.

[gaborcsardi]

@randy3k What is the current status of this action? Is it still broken?

[gaborcsardi]

FWIW, our (Linux) pak builds now work on R installations without a shared library, so I am going to close this.

[github-actions[bot]]

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