precommit deps-in-desc hook failing after upgrade to R 4.3.0 in renv locked package about precommit HOT 12 CLOSED

Thank you @lorenzwalthert for elaborating that process, the troubleshooting process is making more sense now!
I installed styler and also had to do the same for pkgload but it appears that pre-commit install --install-hooks is now going to work (still going, but it's been going for much longer this time).

Thanks for your work on this package! Do you have a means of taking one-off donations?

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thanks for the support @yogat3ch, just to make sure we are on the same page: You selected a monthly donation now.

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Indeed @lorenzwalthert , I decided to donate over time!

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Thanks, I apprecaite that.

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This seems similar to some problems in #476. I just created a wiki page for this problem: https://github.com/lorenzwalthert/precommit/wiki/Packages-are-not-found-after-R-upgrade. Can you follow these steps and let me know if it helps?

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Hi @lorenzwalthert,
Thank you for the gist!
I'm trying to work through it now, and when run pre-commit install --install-hooks it errors.

An unexpected error has occurred: CalledProcessError: command: ('/Library/Frameworks/R.framework/Resources/bin/Rscript', '--vanilla', '-e', '    options(install.packages.compile.from.source = "never", pkgType = "binary")\n            prefix_dir <- \'/Users/stephenholsenbeck/.cache/pre-commit/repo6fq9kgbf\'\n        options(\n            repos = c(CRAN = "https://cran.rstudio.com"),\n            renv.consent = TRUE\n        )\n        source("renv/activate.R")\n        renv::restore()\n        activate_statement <- paste0(\n          \'suppressWarnings({\',\n          \'old <- setwd("\', getwd(), \'"); \',\n          \'source("renv/activate.R"); \',\n          \'setwd(old); \',\n          \'renv::load("\', getwd(), \'");})\'\n        )\n        writeLines(activate_statement, \'activate.R\')\n        is_package <- tryCatch(\n          {\n              path_desc <- file.path(prefix_dir, \'DESCRIPTION\')\n              suppressWarnings(desc <- read.dcf(path_desc))\n              "Package" %in% colnames(desc)\n          },\n          error = function(...) FALSE\n        )\n        if (is_package) {\n            renv::install(prefix_dir)\n        }\n        \n    ')
return code: 1
...
Error: failed to retrieve 'https://api.github.com/repos/r-lib/styler/tarball/96f859daf39f5973851c06506d7827808eea28a8' [cannot open URL 'https://api.github.com/repos/r-lib/styler/tarball/96f859daf39f5973851c06506d7827808eea28a8']
    In addition: Warning messages:
    1: In (function (url, destfile, method, quiet = FALSE, mode = "w",  :
      downloaded length 0 != reported length 0
    2: In (function (url, destfile, method, quiet = FALSE, mode = "w",  :
      cannot open URL 'https://packagemanager.rstudio.com/all/latest/': HTTP status was '404 Not Found'
    3: In (function (url, destfile, method, quiet = FALSE, mode = "w",  :
      downloaded length 0 != reported length 0
    4: In (function (url, destfile, method, quiet = FALSE, mode = "w",  :
      cannot open URL 'https://api.github.com/repos/r-lib/styler/tarball/96f859daf39f5973851c06506d7827808eea28a8': HTTP status was '401 Unauthorized'
    Traceback (most recent calls last):
    8: renv::restore()
    7: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
    6: retrieve(packages)
    5: handler(package, renv_retrieve_impl(package))
    4: renv_retrieve_impl(package)
    3: renv_retrieve_github(record)
    2: renv_retrieve_package(record, url, path)
    1: stop(status)
    Execution halted

I'm seeing that the command appears to be trying to run renv::restore or something based on the stdout I see. It's using an outdated version of renv: 0.16.0, when my repo is running 0.17.2.

  # Bootstrapping renv 0.16.0 --------------------------------------------------
    * Downloading renv 0.16.0 ... OK
    * Installing renv 0.16.0 ... Done!
    * Successfully installed and loaded renv 0.16.0.
    The following package(s) will be updated:

I've attached the log here:
pre-commit.log

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The renv.lock file was snapshotted using R 4.3.0, so those warnings are puzzling.

as per the docs, we don’t touch your renv for the project. It’s a different virtual environment installed in a different directory.

I'm seeing that the command appears to be trying to run renv::restore or something based on the stdout I see. It's using an outdated version of renv: 0.16.0, when my repo is running 0.17.2.

same reason.

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Your next problem seems to relate to your GitHub credentials. If you exceeded the rate limit, then you can try again after some time. Can you try to install that styler package also directly with renv::install(“r-lib/styler@96f859daf39f5973851c06506d7827808eea28a8") anywhere (even in a repo withour renv) to add the package to the cache? If that works successfully, I think you should be able to pre-commit install --install-hooks without problems.

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Im sorry, but I'm not following the reasoning here. Where is pre-commit install --install-hooks running from that it's running renv 0.16.0 and for some reason needs the styler package, and my GITHUB_PAT isn't available to it?

The repo from which I'm running the pre-commit install --install-hooks does not use the styler package, and my github credentials worked fine when I recently renv::restored for this repo.

From the log file error it looks like it's running from a random temp directory?
removing ‘/Users/stephenholsenbeck/.cache/pre-commit/repo6fq9kgbf/renv-default/renv/staging/1/pkgload’

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questions welcome 😄

pre-commit install --install-hooks does:

• clone lorenzwalthert/precommit into its cache and give it a name starting with repo.... On macOS, that repo... lives in ~/.cache/pre-commit/.
• Then, it places an installation script in that repo.
• Then, it runs that script with the working directory being where the script is located, roughly it runs renv::restore().
• As part of running the installation script, it also writes an activation script, that will be executed from your project's working directly, which roughly is 1) change working directory to repo..., 2) renv::load() (which is similar to renv::activate()) and 3) change back to your projects working directory.

When you then run a hook, it sets that activate script as your .Rprofile through an environment variable and executes the hook scripts.

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I don't think your GITHUB_PAT is available now that I think about it because your .Rprofile is not used for running the hooks or isntalling them. That's why I created #486 to avoid depending on GitHub packages in future hook releases.

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Welcome @yogat3ch 😄 . I hope it worked out this time?

I also want to find the source of the problem and improve the user experience, so thanks for helping out. On my GitHub Sponsors page, you can make either recurring or one-off donations:

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