BUG: pre-commit/repoxoi92sgz/node_env-default/bin/node: libc.so.6: version `GLIBC_2.28' not found

[vitkl]

I fail to initialise a repo from this template because pre-commit fails on git commit ....

[INFO] Installing environment for https://github.com/pre-commit/mirrors-prettier.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('~/.cache/pre-commit/repoxoi92sgz/node_env-default/bin/node', '~/.cache/pre-commit/repoxoi92sgz/node_env-default/bin/npm', 'install', '--dev', '--prod', '--ignore-prepublish', '--no-progress', '--no-save')
return code: 1
stdout: (none)
stderr:
    ~/.cache/pre-commit/repoxoi92sgz/node_env-default/bin/node: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.28' not found (required by ~/.cache/pre-commit/repoxoi92sgz/node_env-default/bin/node)

Check the log at ~/.cache/pre-commit/pre-commit.log

The solution presented here jupyterlab/jupyterlab#12675 is adding

default_language_version:
  node: system

to the top of .pre-commit-config.yaml.

However, that solution also fails with:

[INFO] Installing environment for https://github.com/pre-commit/mirrors-prettier.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('npm', 'install', '--dev', '--prod', '--ignore-prepublish', '--no-progress', '--no-save')
return code: 1
stdout:
    Executable `npm` not found
stderr: (none)

I tried to solve this by installing conda install -c conda-forge nodejs - however, this also fails:

prettier.................................................................Failed
- hook id: prettier
- exit code: 1

prettier requires at least version 14 of Node, please upgrade

Is prettier really necessary?

[vitkl]

I deleted prettier from my project https://github.com/vitkl/cell2module, however, I appear to have the same issue with https://github.com/scverse/scvi-tools - where that won't be a solution.

[grst]

Hi @vitkl, thanks for reporting.

Yes, I think we really would like to have prettier -- it takes care of formatting all non-Python files.
We could consider setting the default_language_version. This requires nodejs to be installed on your system which seems to be the reason why it fails for you.

[vitkl]

Do you mean installed via conda install -c conda-forge nodejs or sudo apt install nodejs?

The latter would complicate use - we either need to ask our central IT to keep installing the latest versions or use a singularity image all the time (which requires several steps and devices to build).

[grst]

Both conda and system package manager should work. Personally, I work with the conda version.

[vitkl]

How can my last error be explained?

prettier.................................................................Failed
- hook id: prettier
- exit code: 1

prettier requires at least version 14 of Node, please upgrade

Would be good to see more complete installation instructions in the readme.

[grst]

Well, in theory no installation instructions should be necessary as pre-commit takes care of that. It just installs a node version that is incompatible with your system.

I don't know why you would end up with <v14 when installing it using conda. You can try explicitly requesting a more recent version by using conda install -c conda-forge "nodejs>=14"

[grst]

FWIW, I just found out that it's possible to override the node version using pre-commit:
https://pre-commit.com/#overriding-language-version

Could you please try setting the node version for prettier to an older version of node to find out if it works on your system?

e.g.

    - repo: https://github.com/pre-commit/mirrors-prettier
      rev: v2.5.1
      hooks:
          - id: prettier
            language_version: 16.19.0

[vitkl]

This works, thank you!

    - repo: https://github.com/pre-commit/mirrors-prettier
      rev: v2.5.1
      hooks:
          - id: prettier
            language_version: 16.19.0

[grst]

Perfect! May I ask you to try which is the most recent version of node that still works on your system?
Then I would pin the pre-commit hook to that.

[vitkl]

Do you mean to keep increasing language_version: 16.19.0 until things break?

[grst]

exactly!

Probably it's enough to just specify major numbers, i.e. 17, 18 and it will always use the release within that node version

[vitkl]

17.9.1 still works but 18.0.0 fails:

An unexpected error has occurred: CalledProcessError: command: ('~/.cache/pre-commit/repornsqwln5/node_env-18.0.0/bin/node', '~/.cache/pre-commit/repornsqwln5/node_env-18.0.0/bin/npm', 'install', '--dev', '--prod', '--ignore-prepublish', '--no-progress', '--no-save')
return code: 1
stdout: (none)
stderr:
    ~/.cache/pre-commit/repornsqwln5/node_env-18.0.0/bin/node: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.28' not found (required by ~/.cache/pre-commit/repornsqwln5/node_env-18.0.0/bin/node)

Check the log at ~/.cache/pre-commit/pre-commit.log

[grst]

👍 Thanks!

[grst]

Just one more question: what operating system are you on?

[vitkl]

The system is Ubuntu 18.04 (bionic) (4.15.0-200-generic x86_64).

Actually, I have a problem after using version 17.9.1 to check the code locally - the code style check by prettier fails in a GitHub workflow
https://results.pre-commit.ci/run/github/589381908/1673972697.f9TynPJVRRyjRpt0PpRymw .

Any suggestions about what happened?

[grst]

Ok, then it is as discussed in #144: Ubuntu 18.04 hits end of support this April and is indeed incompatible with the latest node version.

Any suggestions about what happened?

No idea, sorry.

[vitkl]

Maybe this error

prettier.................................................................Failed
- hook id: prettier
- files were modified by this hook

.codecov.yamldocs/contributing.mddocs/MakefileCHANGELOG.md.flake8README.mdsrc/cell2module/models/__init__.py.github/workflows/sync.yaml.bumpversion.cfg.github/ISSUE_TEMPLATE/bug_report.yml.editorconfigpyproject.tomlsrc/cell2module/models/_cell2module_module.py.github/ISSUE_TEMPLATE/feature_request.ymldocs/conf.pydocs/_templates/.gitkeepdocs/_static/.gitkeep.gitignoredocs/make.bat.github/workflows/test.yaml.pre-commit-config.yamlsrc/cell2module/__init__.pydocs/extensions/typed_returns.py.github/ISSUE_TEMPLATE/config.ymldocs/notebooks/example.ipynbdocs/index.md.cruft.json.cruft.json
docs/changelog.mdtests/test_cell2module.pysrc/cell2module/models/_base_module.pydocs/references.bib.github/workflows/build.yamlLICENSEdocs/template_usage.mddocs/api.mddocs/_templates/autosummary/class.rst.readthedocs.yamldocs/references.mdsrc/cell2module/models/_cell2module_model.py

is a result of these files being committed before prettier was run for the first time. It is possible to apply prettier to all files? E.g. like black .

[vitkl]

I found a hack to fix this - just commit changes via a PR such that the workflow is run to automatically modify the files.