Error during environment installation. about precommit HOT 11 CLOSED

Thanks for the report. What's your R version? And is the repo you try to use {precommit} with a public one?

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Hi. Thank you. I'm using R 4.2.2.

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Hi. Pinging as I am still running into this and I am close to submitting the packages to BioConductor

from precommit.

Is this a public repo so I can try to reproduce the problem myself?

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Oh absolutely. CogDisResLab/drugfindR

from precommit.

I can't reproduce your problem on my macOS M1 4.2.1. I get the output of running hooks (some are failing due to style and other issues) inside the RStudio terminal or on a macOS Terminal app. I recommend $ pre-commit clean and then run pre-commit install again, both outside the RStudio terminal.

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Another alternative is to delete all renv caches, but I don't know how that works.

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So this is unusual. I tried both your suggestions but ran into the same issue. It appears that one of the issues I see is that three packages that hit a 404 now have extensions .tar.gz and not .tgz.

    Warning: failed to retrieve 'https://packagemanager.rstudio.com/all/latest/src/contrib/R.cache_0.16.0.tgz' [error code 22]
    Warning: failed to retrieve 'https://packagemanager.rstudio.com/all/latest/src/contrib/R.methodsS3_1.8.2.tgz' [error code 22]
    Warning: failed to retrieve 'https://packagemanager.rstudio.com/all/latest/src/contrib/R.oo_1.25.0.tgz' [error code 22]
    Error: failed to retrieve package '[email protected]'
    In addition: Warning messages:
    1: curl: (22) The requested URL returned error: 404
    2: curl: (22) The requested URL returned error: 404
    3: failed to retrieve 'https://packagemanager.rstudio.com/all/latest/src/contrib/R.cache_0.16.0.tgz' [error code 22]
    4: curl: (22) The requested URL returned error: 404
    5: failed to retrieve 'https://packagemanager.rstudio.com/all/latest/src/contrib/R.methodsS3_1.8.2.tgz' [error code 22]
    6: curl: (22) The requested URL returned error: 404
    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_repos(record)
    2: stopf("failed to retrieve package '%s'", renv_record_format_remote(record))
    1: stop(sprintf(fmt, ...), call. = call.)
    Execution halted

from precommit.

Yeah I also noted that. I am not familiar enough with CRAN to know what that means. But I don't know if it's unusual. Also, these packages are not archived, i.e. our requirement is the latest version on CRAN. Another thing you can try is to purge and re-install the packages:

purrr::walk(c("[email protected]", "[email protected]", "[email protected]"), function(pkg) {
  renv::purge(pkg)
  renv::install(pkg)
})

This can be done in any renv or outside an active {renv} project. Maybe this will help? If not, retry wit pre-commit clean after the purge/install step.

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So I used the trick of individually purging and reinstalling the renv packages and ran into more such errors. I repeated the process and now have it running without issue. Thank you.

I'm unsure what the issue was but it is solved now. It may be linked to the "Additional packages" list for the roxygen hook. I'll keep you updated. I think we can resolve this here.

Thank you for the excellent package and your prompt and helpful responses.

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Glad it worked for you. Seems like the general solution to delete all renv infra is described in this StackOverflow answer:

root <- renv::paths$root()
unlink(root, recursive = TRUE)
utils::remove.packages("renv")

I still think that maybe the R version is the root cause for the problem. Ie you upgrade R and the linked installed binaries are not there or something like this. Let’s see if others run into this problem too.

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