Failed to get R devel: Failed to get R 4.5.0 (Mac 14)

[pachadotdev]

Yesteday, the CI was working ok for this test https://github.com/pachadotdev/open-redatam/actions/runs/11943074392/job/33291401262

Now it displays

Run r-lib/actions/setup-r@v2
  with:
    r-version: devel
    use-public-rspm: true
    Ncpus: 1
    remove-openmp-macos: true
    install-r: true
    windows-path-include-rtools: true
    windows-path-include-mingw: true
    update-rtools: false
    working-directory: .
  env:
    GITHUB_PAT: ***
    R_KEEP_PKG_SOURCE: yes
Downloading gfortran
Downloading macOS utils
Error: Failed to get R devel: Failed to get R 4.5.0: Failed to install qpdf: Error: The process '/opt/homebrew/bin/brew' failed with exit code 1

[gaborcsardi]

Why do you think that this is a bug in r-hub/actions and not a failed download due to a network error or a bug in homebrew?

[ygeunkim]

This seems related to #950 but I'm experiencing the same issue only with {os: macOS-latest, r: 'release'} configuration. The check fails during setup-r step due to qpdf installation failure.

[tmorrell]

I started seeing this in my macOS runs yesterday, and it seems to be getting worse today (75% failure rate). There isn't anything useful in the output even with debug logging on

::group::Downloading macOS utils
Downloading macOS utils
  ##[debug]Error: The process '/opt/homebrew/bin/brew' failed with exit code 1
  ::endgroup::
##[debug]Failed to install qpdf: Error: The process '/opt/homebrew/bin/brew' failed with exit code 1
##[debug]Failed to get R 4.4.2: Failed to install qpdf: Error: The process '/opt/homebrew/bin/brew' failed with exit code 1
Error: Failed to get R release: Failed to get R 4.4.2: Failed to install qpdf: Error: The process '/opt/homebrew/bin/brew' failed with exit code 1
##[debug]Node Action run completed with exit code 1
##[debug]Finishing: Run r-lib/actions/setup-r@v2

[nvelden]

I have the same issue.

[dylanhmorris]

Why do you think that this is a bug in r-hub/actions and not a failed download due to a network error or a bug in homebrew?

At least for me, downgrading the GH hosted runner from macos-latest to macos-13 appears to be a solid workaround. I note that the macos-13 runner ships with Homebrew 4.4.4 (whereas macos-14/macos-latest ships with Homebrew 4.4.5). There's at least one other potentially important difference, though: I believe that macos-13 is x86 while macos-14 and up are arm64

[pachadotdev]

Why do you think that this is a bug in r-hub/actions and not a failed download due to a network error or a bug in homebrew?

At least for me, downgrading the GH hosted runner from macos-latest to macos-13 appears to be a solid workaround. I note that the macos-13 runner ships with Homebrew 4.4.4 (whereas macos-14/macos-latest ship with Homebrew 4.4.5). There's at least one other potentially important difference, though: I believe that macos-13 is x86 while macos-14 and up are arm64

yes, 14 is arm and 13 is x64

[pachadotdev]

Why do you think that this is a bug in r-hub/actions and not a failed download due to a network error or a bug in homebrew?

I repeated the test on separate days

[tmorrell]

I think this is difficult to debug because of the silent at

actions/setup-r/src/installer.ts

Line 261 in e8c6069

], { silent: true });

I've been unable to test changing this because there aren't instructions for generating the dist js files

[gaborcsardi]

This is an error either in Homebrew or the runner image (version 20241119.509). The latest runner image (20241022.361) fixes this, it is being deployed right now. Deployment is a long process, so it might still be happening for some time.

No need to report this again, unless it happens with the new image.

Also no need to add "me too" comments without any additional information.

[krlmlr]

Another workaround is to run

brew uninstall pkg-config@0.29.2

before installing R.

Successful run: https://github.com/krlmlr/bindr/actions/runs/11994406964/job/33436418065?pr=16#step:7:266 .

The installation error comes from linking conflicts between pkg-config@0.29.2 and pkgconfig . From a debugging session:

$ brew install pkgconfig
==> Downloading https://ghcr.io/v2/homebrew/core/pkgconf/manifests/2.3.0_1
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/2d395f41484daa2c37c818f7abd9d0fc8dd82ff2892c542d9eb136b442ebae19--pkgconf-2.3.0_1.bottle_manifest.json
==> Fetching pkgconf
==> Downloading https://ghcr.io/v2/homebrew/core/pkgconf/blobs/sha256:5f83615f295e78e593c767d84f3eddf61bfb0b849a1e6a5ea343506b30b2c620
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/9feec073ca999cd99c8ddd43a9654742184c761fa3caf57feb23ae9fe2937344--pkgconf--2.3.0_1.arm64_sonoma.bottle.tar.gz
==> Pouring pkgconf--2.3.0_1.arm64_sonoma.bottle.tar.gz
::error::The `brew link` step did not complete successfully
The formula built, but is not symlinked into /opt/homebrew
Could not symlink bin/pkg-config
Target /opt/homebrew/bin/pkg-config
is a symlink belonging to pkg-config@0.29.2. You can unlink it:
  brew unlink pkg-config@0.29.2

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

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

Possible conflicting files are:
/opt/homebrew/bin/pkg-config -> /opt/homebrew/Cellar/pkg-config@0.29.2/0.29.2_3/bin/pkg-config
/opt/homebrew/share/aclocal/pkg.m4 -> /opt/homebrew/Cellar/pkg-config@0.29.2/0.29.2_3/share/aclocal/pkg.m4
/opt/homebrew/share/man/man1/pkg-config.1 -> /opt/homebrew/Cellar/pkg-config@0.29.2/0.29.2_3/share/man/man1/pkg-config.1
==> Summary
🍺  /opt/homebrew/Cellar/pkgconf/2.3.0_1: 27 files, 474KB

[pachadotdev]

Another workaround is to run

brew uninstall pkg-config@0.29.2

before installing R.

Successful run: https://github.com/krlmlr/bindr/actions/runs/11994406964/job/33436418065?pr=16#step:7:266 .

The installation error comes from linking conflicts between pkg-config@0.29.2 and pkgconfig . From a debugging session:

$ brew install pkgconfig
==> Downloading https://ghcr.io/v2/homebrew/core/pkgconf/manifests/2.3.0_1
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/2d395f41484daa2c37c818f7abd9d0fc8dd82ff2892c542d9eb136b442ebae19--pkgconf-2.3.0_1.bottle_manifest.json
==> Fetching pkgconf
==> Downloading https://ghcr.io/v2/homebrew/core/pkgconf/blobs/sha256:5f83615f295e78e593c767d84f3eddf61bfb0b849a1e6a5ea343506b30b2c620
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/9feec073ca999cd99c8ddd43a9654742184c761fa3caf57feb23ae9fe2937344--pkgconf--2.3.0_1.arm64_sonoma.bottle.tar.gz
==> Pouring pkgconf--2.3.0_1.arm64_sonoma.bottle.tar.gz
::error::The `brew link` step did not complete successfully
The formula built, but is not symlinked into /opt/homebrew
Could not symlink bin/pkg-config
Target /opt/homebrew/bin/pkg-config
is a symlink belonging to pkg-config@0.29.2. You can unlink it:
  brew unlink pkg-config@0.29.2

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

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

Possible conflicting files are:
/opt/homebrew/bin/pkg-config -> /opt/homebrew/Cellar/pkg-config@0.29.2/0.29.2_3/bin/pkg-config
/opt/homebrew/share/aclocal/pkg.m4 -> /opt/homebrew/Cellar/pkg-config@0.29.2/0.29.2_3/share/aclocal/pkg.m4
/opt/homebrew/share/man/man1/pkg-config.1 -> /opt/homebrew/Cellar/pkg-config@0.29.2/0.29.2_3/share/man/man1/pkg-config.1
==> Summary
🍺  /opt/homebrew/Cellar/pkgconf/2.3.0_1: 27 files, 474KB

Kirill sapbe! thanks a lot

[jcheng5]

This is an error either in Homebrew or the runner image (version 20241119.509). The latest runner image (20241022.361) fixes this, it is being deployed right now.

Is that not backwards? 20241119.509 is the latest, and it's the one that's breaking; 20241022.361 is the one that used to work.

[gaborcsardi]

That would indeed make a lot of sense....

[glatterf42]

Possibly related: Homebrew/brew#18788
Which might imply that a new brew release could fix this issue, but it might also mean another month before that makes it into a new runner image.

[github-actions]

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