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Conflicts with r-lib/actions/setup-r on macOS #375

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khaeru opened this issue Sep 22, 2022 · 2 comments
Open

Conflicts with r-lib/actions/setup-r on macOS #375

khaeru opened this issue Sep 22, 2022 · 2 comments
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bug Something isn't working help wanted Extra attention is needed

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@khaeru
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khaeru commented Sep 22, 2022

Describe the bug

In this workflow, we use both r-lib/actions/setup-r and setup-graphviz.

Recently the workflow began to error on macOS only; the key lines are:

==> Upgrading 1 dependent of upgraded formulae:
Disable this behaviour by setting HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK.
Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`).
r 4.2.1_3 -> 4.2.1_4
==> Downloading https://ghcr.io/v2/homebrew/core/r/manifests/4.2.1_4
==> Downloading https://ghcr.io/v2/homebrew/core/r/blobs/sha256:a5d64662b14c9669f3a58f1c6ad30982db60d681e299a5163780af6c313c3835
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sha256:a5d64662b14c9669f3a58f1c6ad30982db60d681e299a5163780af6c313c3835?se=2022-09-22T20%3A35%3A00Z&sig=zrLxcUkU1ehB8yeQmwlfdbuQC3MZZNZILZVDE%2B4IpJs%3D&sp=r&spr=https&sr=b&sv=2019-12-12
==> Upgrading r
  4.2.1_3 -> 4.2.1_4 

==> Pouring r--4.2.1_4.big_sur.bottle.tar.gz
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/R
Target /usr/local/bin/R
already exists. You may want to remove it:
  rm '/usr/local/bin/R'

To force the link and overwrite all conflicting files:
  brew link --overwrite r

To list all files that would be deleted:
  brew link --overwrite --dry-run r

Possible conflicting files are:
/usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R
/usr/local/bin/Rscript -> /Library/Frameworks/R.framework/Resources/bin/Rscript

To Reproduce

Steps to reproduce the behavior:

# In an action

jobs:
  job-name:
    steps:
    - uses: r-lib/actions/setup-r@v2
    - uses: ts-graphviz/[email protected]

Expected behavior

Both are installed and usable on the job runner.

I was able to work around the error by reversing the order: setup-graphviz before setup-r. Usability would be better if the actions were not sensitive to order.

@kamiazya kamiazya pinned this issue Oct 14, 2022
khaeru added a commit to iiasa/message_ix that referenced this issue Nov 2, 2022
@kamiazya
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kamiazya commented Jan 5, 2023

@all-contributors please add @khaeru for bug, research.

@allcontributors
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@kamiazya

I've put up a pull request to add @khaeru! 🎉

@kamiazya kamiazya added bug Something isn't working help wanted Extra attention is needed labels Oct 7, 2023
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