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Brew attempts and fails to install python on macos-13 runners #630

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khaeru opened this issue Jun 17, 2024 · 2 comments
Open

Brew attempts and fails to install python on macos-13 runners #630

khaeru opened this issue Jun 17, 2024 · 2 comments
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help wanted Extra attention is needed

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@khaeru
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khaeru commented Jun 17, 2024

Describe the bug

I see the following when using the action in a workflow that runs on: macos-13.

Run ts-graphviz/setup-graphviz@v2
  with:
    macos-skip-brew-update: true
    ubuntu-skip-apt-update: false
  env:
    depth: 100
/usr/local/bin/brew install graphviz
==> Downloading https://ghcr.io/v2/homebrew/core/graphviz/manifests/11.0.0
==> Fetching dependencies for graphviz: jasper, netpbm, gts, gdk-pixbuf, fribidi, pango and librsvg
==> Downloading https://ghcr.io/v2/homebrew/core/jasper/manifests/4.2.4
==> Fetching jasper
==> Downloading https://ghcr.io/v2/homebrew/core/jasper/blobs/sha256:18d3d583cb960f8e4872ffc5b2181b6282f95d2c1ebd3a659d0e0b3edf55bc10
==> Downloading https://ghcr.io/v2/homebrew/core/netpbm/manifests/11.02.09
==> Fetching netpbm
==> Downloading https://ghcr.io/v2/homebrew/core/netpbm/blobs/sha256:1eb8e095b030db593891e7ccd136d035f16f3555b29d97f6df470032f2f92c3a
==> Downloading https://ghcr.io/v2/homebrew/core/gts/manifests/0.7.6_3
==> Fetching dependencies for gts: [email protected]
==> Downloading https://ghcr.io/v2/homebrew/core/python/3.12/manifests/3.12.4
==> Fetching [email protected]
==> Downloading https://ghcr.io/v2/homebrew/core/python/3.12/blobs/sha256:93d81dfa181e6890b6a2baa4fbb4df71b6c061a2dc7823fe0ae12b2ec4b59cc1
==> Fetching gts
==> Downloading https://ghcr.io/v2/homebrew/core/gts/blobs/sha256:946d3f08c41e94c2861e555358fd152df7c069ad8a2a7f621b64b55cfb8ceffb
==> Downloading https://ghcr.io/v2/homebrew/core/gdk-pixbuf/manifests/2.42.12
==> Fetching gdk-pixbuf
==> Downloading https://ghcr.io/v2/homebrew/core/gdk-pixbuf/blobs/sha256:80e5eacf286d8371d7fcc13cc9b79d4612ded6d0db3398c5741790174ae70f85
==> Downloading https://ghcr.io/v2/homebrew/core/fribidi/manifests/1.0.15
==> Fetching fribidi
==> Downloading https://ghcr.io/v2/homebrew/core/fribidi/blobs/sha256:664ed32cf6eb7682b3ff7e86bd4fb3df5f86eb97ebfecf136c6312479c5b15bd
==> Downloading https://ghcr.io/v2/homebrew/core/pango/manifests/1.54.0
==> Fetching pango
==> Downloading https://ghcr.io/v2/homebrew/core/pango/blobs/sha256:11d51f9281cd68d0b8718158df55bc28029e25956f1ad313cae99b31ae130dbb
==> Downloading https://ghcr.io/v2/homebrew/core/librsvg/manifests/2.58.1
==> Fetching librsvg
==> Downloading https://ghcr.io/v2/homebrew/core/librsvg/blobs/sha256:2350745eca6a4b73982e9e8c40f4924f5eff08bb43380f4dda54e2586fa19a71
==> Fetching graphviz
==> Downloading https://ghcr.io/v2/homebrew/core/graphviz/blobs/sha256:e0a790680fbfa22a93b1fc73c7e6f5ca71bc115dacb84cfbf9409c80ee16ec89
==> Installing dependencies for graphviz: jasper, netpbm, gts, gdk-pixbuf, fribidi, pango and librsvg
==> Installing graphviz dependency: jasper
==> Downloading https://ghcr.io/v2/homebrew/core/jasper/manifests/4.2.4
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/0edc7047fdbd9e0fd88f4c5ceed204b57e9b4d4f42c1b1b21c502d68fce31118--jasper-4.2.4.bottle_manifest.json
==> Pouring jasper--4.2.4.ventura.bottle.tar.gz
🍺  /usr/local/Cellar/jasper/4.2.4: 45 files, 1.5MB
==> Installing graphviz dependency: netpbm
==> Downloading https://ghcr.io/v2/homebrew/core/netpbm/manifests/11.02.09
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/1c4be61c6a2db4fdbc7e0252e62cd50fb8296d87a1cc919668ac3c70c6ff7e7f--netpbm-11.02.09.bottle_manifest.json
==> Pouring netpbm--11.02.09.ventura.bottle.tar.gz
🍺  /usr/local/Cellar/netpbm/11.02.09: 417 files, 12.9MB
==> Installing graphviz dependency: gts
==> Downloading https://ghcr.io/v2/homebrew/core/gts/manifests/0.7.6_3
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/0cb7519523b42ff855917c33218c1ef771e3060080fea895de59eb848c833cd1--gts-0.7.6_3.bottle_manifest.json
==> Installing dependencies for gts: [email protected]
==> Installing gts dependency: [email protected]
==> Downloading https://ghcr.io/v2/homebrew/core/python/3.12/manifests/3.12.4
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/2970a992f26f411cf71250ce54eb24411d8b065824b51819da7085559f09ce66--python@3.12-3.12.4.bottle_manifest.json
==> Pouring [email protected]
Error: The `brew link` step did not complete successfully
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/2to3
Target /usr/local/bin/2to3
already exists. You may want to remove it:
  rm '/usr/local/bin/2to3'

To force the link and overwrite all conflicting files:
  brew link --overwrite [email protected]

To list all files that would be deleted:
  brew link --overwrite [email protected] --dry-run

Possible conflicting files are:
/usr/local/bin/2to3 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/2to3
/usr/local/bin/2to3-3.12 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/2to3-3.12
/usr/local/bin/idle3 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/idle3
/usr/local/bin/idle3.12 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/idle3.12
/usr/local/bin/pydoc3 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/pydoc3
/usr/local/bin/pydoc3.12 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/pydoc3.12
/usr/local/bin/python3 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/python3
/usr/local/bin/python3-config -> /Library/Frameworks/Python.framework/Versions/3.12/bin/python3-config
/usr/local/bin/python3.12 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12
/usr/local/bin/python3.12-config -> /Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12-config
==> /usr/local/Cellar/[email protected]/3.12.4/bin/python3.12 -Im ensurepip
==> /usr/local/Cellar/[email protected]/3.12.4/bin/python3.12 -Im pip install -v --no-
==> Summary
🍺  /usr/local/Cellar/[email protected]/3.12.4: 3,277 files, 63.9MB
==> Installing gts
==> Pouring gts--0.7.6_3.ventura.bottle.tar.gz
🍺  /usr/local/Cellar/gts/0.7.6_3: 27 files, 1.4MB
==> Installing graphviz dependency: gdk-pixbuf
==> Downloading https://ghcr.io/v2/homebrew/core/gdk-pixbuf/manifests/2.42.12
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/51502ca3ad1b3a076e2aec3be882089fbd1c2257b822a0d3c155e23e68a7e70e--gdk-pixbuf-2.42.12.bottle_manifest.json
==> Pouring gdk-pixbuf--2.42.12.ventura.bottle.tar.gz
==> /usr/local/Cellar/gdk-pixbuf/2.42.12/bin/gdk-pixbuf-query-loaders --update-c
🍺  /usr/local/Cellar/gdk-pixbuf/2.42.12: 152 files, 3.8MB
==> Installing graphviz dependency: fribidi
==> Downloading https://ghcr.io/v2/homebrew/core/fribidi/manifests/1.0.15
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/c743b3178050604a607c1ebc433b1b187bb5250afa047857b62467fb9f62249a--fribidi-1.0.15.bottle_manifest.json
==> Pouring fribidi--1.0.15.ventura.bottle.tar.gz
🍺  /usr/local/Cellar/fribidi/1.0.15: 68 files, 703.6KB
==> Installing graphviz dependency: pango
==> Downloading https://ghcr.io/v2/homebrew/core/pango/manifests/1.54.0
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/06c4532b8d175a9098d6a1c5b6b1d2b154b126fef30ddbb5b26791e86b8c9675--pango-1.54.0.bottle_manifest.json
==> Pouring pango--1.54.0.ventura.bottle.tar.gz
🍺  /usr/local/Cellar/pango/1.54.0: 69 files, 3.3MB
==> Installing graphviz dependency: librsvg
==> Downloading https://ghcr.io/v2/homebrew/core/librsvg/manifests/2.58.1
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/33310076ed8eb156ee41e99f2dc398e83fffb55bcbf9dfc51dc6145e9bd0ee08--librsvg-2.58.1.bottle_manifest.json
==> Pouring librsvg--2.58.1.ventura.bottle.tar.gz
==> /usr/local/opt/gdk-pixbuf/bin/gdk-pixbuf-query-loaders --update-cache
🍺  /usr/local/Cellar/librsvg/2.58.1: 23 files, 46.4MB
==> Installing graphviz
==> Pouring graphviz--11.0.0.ventura.bottle.tar.gz
🍺  /usr/local/Cellar/graphviz/11.0.0: 283 files, 6.5MB
Error: The process '/usr/local/bin/brew' failed with exit code 1

To Reproduce

I have not made an effort to reproduce this outside of the repo in which it is encountered, e.g. in a new/blank repo.

Expected behavior

Graphviz is installed.

Additional context

  • Note that I am using the macos-skip-brew-update: true input.
  • Previously I filed the similar Conflicts with r-lib/actions/setup-r on macOS #375. There, the work-around was to put the setup-graphviz step before setup-R. Here, this does not work.
  • The workflow in question runs on macos-13 (x86_64 architecture), not macos-latest (arm64).
@khaeru khaeru mentioned this issue Jun 17, 2024
Merged
2 tasks
khaeru added a commit to iiasa/ixmp that referenced this issue Jun 17, 2024
@khaeru
Work around ts-graphviz/setup-graphviz#630
d4b3fee
khaeru added a commit to iiasa/ixmp that referenced this issue Jun 17, 2024
@khaeru
Work around ts-graphviz/setup-graphviz#630
b085f49
khaeru added a commit to iiasa/message_ix that referenced this issue Jun 17, 2024
@khaeru
Work around ts-graphviz/setup-graphviz#630
1784395
@khaeru khaeru mentioned this issue Jun 17, 2024
Merged
2 tasks
khaeru added a commit to iiasa/message_ix that referenced this issue Jun 17, 2024
@khaeru
Work around ts-graphviz/setup-graphviz#630
789ba55
khaeru added a commit to iiasa/message_ix that referenced this issue Jun 17, 2024
@khaeru
Work around ts-graphviz/setup-graphviz#630
c9df55e
khaeru added a commit to iiasa/message-ix-models that referenced this issue Jun 17, 2024
@khaeru
Work around ts-graphviz/setup-graphviz#630
2820ab0
@khaeru khaeru mentioned this issue Jun 17, 2024
Merged
2 tasks
@kamiazya kamiazya added the help wanted Extra attention is needed label Jun 17, 2024
@khaeru khaeru changed the title Brew attempts and fails to install python on macOS runners Brew attempts and fails to install python on macos-13 runners Jun 18, 2024
@khaeru
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khaeru commented Jun 18, 2024

For additional information, here is a workflow https://github.com/khaeru/genno/actions/runs/9559286674 in which this action is used with both macos-latest and macos-13 runners.

The jobs on macos-latest succeed; the ones on macos-13 fail. So I believe I am only seeing failures in the latter case and have updated the issue title.

Pending any fix, could a maintainer please let us know:

  • Is this action intended to work on all GitHub's runner images, or only a subset? If so, which ones?
  • Is it tested on macos-13?

khaeru added a commit to khaeru/genno that referenced this issue Jun 19, 2024
@khaeru
Work around ts-graphviz/setup-graphviz#630
a56dc27
khaeru added a commit to khaeru/genno that referenced this issue Jun 19, 2024
@khaeru
Work around ts-graphviz/setup-graphviz#630
10eee47
khaeru added a commit to khaeru/genno that referenced this issue Jun 19, 2024
@khaeru
Work around ts-graphviz/setup-graphviz#630
a6fde1c
@kamiazya
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@khaeru
Thank you for bringing this issue to our attention.

Currently, the setup-graphviz action is tested on the following environments: ubuntu-latest, windows-latest, and macos-latest. Unfortunately, macos-13 is not supported at this time, which is likely causing the issues you are encountering. We recommend using the supported environments for optimal results.

For further details on the tested environments and workflow configurations, please refer to our workflow.yaml.

khaeru added a commit to iiasa/message-ix-models that referenced this issue Nov 20, 2024
@khaeru
Adjust workaround for ts-graphviz/setup-graphviz#630
b42ef1a 
Only skip install on macos-13; allow on macos-latest.
khaeru added a commit to iiasa/message-ix-models that referenced this issue Nov 21, 2024
@khaeru
Adjust workaround for ts-graphviz/setup-graphviz#630
0e688c3 
Only skip install on macos-13; allow on macos-latest.
ywpratama pushed a commit to ywpratama/message_ix that referenced this issue Jan 15, 2025
@khaeru @ywpratama
Work around ts-graphviz/setup-graphviz#630
dbf6c0b
khaeru added a commit to iiasa/ixmp that referenced this issue Jan 20, 2025
@khaeru
Use astral-sh/setup-uv in "pytest" GHA workflow
9f2e9dd 
- Discard commented workflow contents for pandas 2.0.0 pre-release.
- Reduce scope of exclusion for ts-graphviz/setup-graphviz#630
  workaround.
- Use env.UV_PYTHON from setup-uv instead of pythonLocation.
- Drop workaround for pyam-iamc exclusion of Python 3.13.
- Add --durations=20 to pytest invocation.
- Drop use of CODECOV_TOKEN.
khaeru added a commit to iiasa/ixmp that referenced this issue Jan 20, 2025
@khaeru
Use astral-sh/setup-uv in "pytest" GHA workflow
de5d4b9 
- Discard commented workflow contents for pandas 2.0.0 pre-release.
- Reduce scope of exclusion for ts-graphviz/setup-graphviz#630
  workaround.
- Use env.UV_PYTHON from setup-uv instead of pythonLocation.
- Drop workaround for pyam-iamc exclusion of Python 3.13.
- Add --durations=20 to pytest invocation.
- Drop use of CODECOV_TOKEN.
khaeru added a commit to iiasa/ixmp that referenced this issue Jan 20, 2025
@khaeru
Use astral-sh/setup-uv in "pytest" GHA workflow
039fa82 
- Discard commented workflow contents for pandas 2.0.0 pre-release.
- Reduce scope of exclusion for ts-graphviz/setup-graphviz#630
  workaround.
- Use Python location from setup-uv instead of $pythonLocation.
- Drop workaround for pyam-iamc exclusion of Python 3.13.
- Add --durations=20 to pytest invocation.
khaeru added a commit to iiasa/ixmp that referenced this issue Jan 20, 2025
@khaeru
Use astral-sh/setup-uv in "pytest" GHA workflow
20e63cb 
- Discard commented workflow contents for pandas 2.0.0 pre-release.
- Reduce scope of exclusion for ts-graphviz/setup-graphviz#630
  workaround.
- Use Python location from setup-uv instead of $pythonLocation.
- Drop workaround for pyam-iamc exclusion of Python 3.13.
- Add --durations=20 to pytest invocation.
- Drop workaround for codecov/codecov-action#1316.
khaeru added a commit to iiasa/ixmp that referenced this issue Jan 20, 2025
@khaeru
Use astral-sh/setup-uv in "pytest" GHA workflow
d0efe14 
- Discard commented workflow contents for pandas 2.0.0 pre-release.
- Reduce scope of exclusion for ts-graphviz/setup-graphviz#630
  workaround.
- Use Python location from setup-uv instead of $pythonLocation.
- Drop workaround for pyam-iamc exclusion of Python 3.13.
- Add --durations=20 to pytest invocation.
- Drop workaround for codecov/codecov-action#1316.
khaeru added a commit to iiasa/message_ix that referenced this issue Jan 21, 2025
@khaeru
Use astral-sh/setup-uv in "pytest" GHA workflow
0a4b17e 
- Drop old content:
  - Commented GAMS_VERSION.
  - Workaround for pyam-iamc exclusion of Python 3.13.
- Narrow workaround for ts-graphviz/setup-graphviz#630.
- Adjust 'tutorials' jobs parallel to #909, #910.
- Simplify installation of reticulate.
  - Drop use of "remotes"; call install.packages() directly.
khaeru added a commit to iiasa/message_ix that referenced this issue Jan 21, 2025
@khaeru
Use astral-sh/setup-uv in "pytest" GHA workflow
4adab48 
- Drop old content:
  - Commented GAMS_VERSION.
  - Workaround for pyam-iamc exclusion of Python 3.13.
- Narrow workaround for ts-graphviz/setup-graphviz#630.
- Adjust 'tutorials' jobs parallel to #909, #910.
- Simplify installation of reticulate.
  - Drop use of "remotes"; call install.packages() directly.
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