xfun: conflicts with xfun@0.53

[BjarkeHautop]

Before filing a bug

• I have installed the latest dev version of {precommit} with remotes::install_github('lorenzwalthert/precommit')
• I have installed the latest hook revisions (update with precommit::autoupdate())
• I have installed the latest release of the upstream Python framework pre-comit as described under the update instructions.

Describe the bug
Dependency errors when using precommit. Says xfun: conflicts with xfun@0.53

$ git commit -m "test"
[INFO] Initializing environment for https://github.com/lorenzwalthert/precommit.
[INFO] Initializing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Initializing environment for https://github.com/pre-commit-ci/pre-commit-ci-config.
[INFO] Installing environment for https://github.com/lorenzwalthert/precommit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('C:/PROGRA1/R/R-451.1\bin\Rscript.exe', '--vanilla', 'C:\Users\name\AppData\Local\Temp\tmp_fkmnpbn\script.R')
return code: 1
stdout:
# Bootstrapping renv 1.1.5 ---------------------------------------------------
- Downloading renv ... OK
- Installing renv ... OK

- One or more packages recorded in the lockfile are not installed.
- Use `renv::status()` for more details.
The following package(s) will be installed:
- pak [0.9.0]
These packages will be installed into "~/.cache/pre-commit/reponkl02hgo/renv-default/renv/library/windows/R-4.5/x86_64-w64-mingw32".

# Installing packages --------------------------------------------------------
- Installing pak ...                            OK [linked from cache]
Successfully installed 1 package in 14 milliseconds.
Traceback (most recent calls last):
6: renv::restore()
5: renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclude,
       prompt = prompt, project = project)
4: pak$pkg_install(pkg = remotes, ask = prompt)
3: remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...),
       list(pkg = pkg, lib = lib, upgrade = upgrade, ask = ask,
           start = start, dependencies = dependencies, loaded = loaded_packages(lib)))
2: err$throw(res$error)
1: base::stop(cond)

stderr:
ℹ Loading metadata database
✔ Loading metadata database ... done

Error:
! error in pak subprocess
Caused by error:
! Could not solve package dependencies:
* R.cache@0.17.0: dependency conflict
* R.methodsS3@1.8.2: dependency conflict
* R.oo@1.27.1: dependency conflict
* R.utils@2.13.0: dependency conflict
* R6@2.6.1: dependency conflict
* Rcpp@1.1.0: dependency conflict
* V8@8.0.1: dependency conflict
* callr@3.7.6: dependency conflict
* commonmark@2.0.0: dependency conflict
* cpp11@0.5.2: dependency conflict
* curl@7.0.0: dependency conflict
* desc@1.4.3: dependency conflict
* digest@0.6.37: dependency conflict
* docopt@0.7.2: dependency conflict
* purrr@1.1.0: dependency conflict
* pkgbuild@1.4.8: dependency conflict
* magrittr@2.0.4: dependency conflict
* processx@3.8.6: dependency conflict
* ps@1.9.1: dependency conflict
* pkgload@1.4.1: dependency conflict
* xmlparsedata@1.0.5: dependency conflict
* brew@1.0-10: dependency conflict
* cli@3.6.5: dependency conflict
* codetools@0.2-20: dependency conflict
* highr@0.11: Can't install dependency xfun (>= 0.18)
* xfun: Conflicts with xfun@0.53
* knitr@1.50: Can't install dependency xfun (>= 0.51)
* ...

$ pre-commit --version
pre-commit 4.3.0

To Reproduce
Steps to reproduce the behavior:

1. Make a new R package using package template from RStudio: File -> New project... -> New directory -> New R package
2. Use precommit:

library(precommit)
use_precommit()
ℹ Using local config from C:/Users/name/AppData/Local/R/win-library/4.5/precommit/pre-commit-config-pkg.yaml.
✔ Copied .pre-commit-config.yaml to C:/Users/name/Documents/GitHub/rprecommit
✔ Adding ^.pre-commit-config.yaml$ to C:/Users/name/Documents/GitHub/rprecommit/.Rbuildignore.
• Edit .precommit-config.yaml to (de)activate the hooks you want to use.
• All available hooks: https://pre-commit.com/hooks.html
• R specific hooks: https://github.com/lorenzwalthert/precommit
✔ Ran pre-commit autoupdate () to get the latest version of the hooks.
ℹ Installing hooks in non-blocking background process. If you experience problems or prefer a blocking process, use options("precommit.block_install_hooks" = TRUE).
• Sign in with GitHub to authenticate https://pre-commit.ci and then come back to complete the set-up process. • It seems like you are using the roxygenize hook. This requires further edits in your .pre-commit-config.yaml, please run precommit::snippet_generate('additional-deps-roxygenize') to proceed.
precommit::snippet_generate('additional-deps-roxygenize')
Generating snippet using CRAN versions. If you need another source, specify with syntax that renv::install() understands (see examples in help file).
✔ According to `DESCRIPTION``, there are no hard dependencies of your package. You are set.
NULL

3. Commit with git:

$ git add .
warning: in the working copy of '.Rbuildignore', CRLF will be replaced by LF the next time Git touches it
warning: in the working copy of '.gitignore', CRLF will be replaced by LF the next time Git touches it
warning: in the working copy of 'DESCRIPTION', CRLF will be replaced by LF the next time Git touches it
warning: in the working copy of 'NAMESPACE', CRLF will be replaced by LF the next time Git touches it
warning: in the working copy of 'R/hello.R', CRLF will be replaced by LF the next time Git touches it
warning: in the working copy of 'man/hello.Rd', CRLF will be replaced by LF the next time Git touches it
warning: in the working copy of 'rprecommit.Rproj', CRLF will be replaced by LF the next time Git touches it

$ git commit -m "test"
[INFO] Locking pre-commit directory
[INFO] Installing environment for https://github.com/lorenzwalthert/precommit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('C:/PROGRA1/R/R-451.1\bin\Rscript.exe', '--vanilla', 'C:\Users\name\AppData\Local\Temp\tmpejlzrqbv\script.R')
return code: 1
stdout:
# Bootstrapping renv 1.1.5 ---------------------------------------------------
- Downloading renv ... OK
- Installing renv ... OK

- One or more packages recorded in the lockfile are not installed.
- Use `renv::status()` for more details.
The following package(s) will be installed:
- pak [0.9.0]
These packages will be installed into "~/.cache/pre-commit/reponkl02hgo/renv-default/renv/library/windows/R-4.5/x86_64-w64-mingw32".

# Installing packages --------------------------------------------------------
- Installing pak ...                            OK [linked from cache]
Successfully installed 1 package in 35 milliseconds.
Traceback (most recent calls last):
6: renv::restore()
5: renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclude,
       prompt = prompt, project = project)
4: pak$pkg_install(pkg = remotes, ask = prompt)
3: remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...),
       list(pkg = pkg, lib = lib, upgrade = upgrade, ask = ask,
           start = start, dependencies = dependencies, loaded = loaded_packages(lib)))
2: err$throw(res$error)
1: base::stop(cond)

stderr:
ℹ Loading metadata database
✔ Loading metadata database ... done

Error:
! error in pak subprocess
Caused by error:
! Could not solve package dependencies:
* R.cache@0.17.0: dependency conflict
* R.oo@1.27.1: dependency conflict
* R6@2.6.1: dependency conflict
* Rcpp@1.1.0: dependency conflict
* R.utils@2.13.0: dependency conflict
* R.methodsS3@1.8.2: dependency conflict
* V8@8.0.1: dependency conflict
* backports@1.5.0: dependency conflict
* cli@3.6.5: dependency conflict
* codetools@0.2-20: dependency conflict
* digest@0.6.37: dependency conflict
* here@1.0.2: dependency conflict
* highr@0.11: Can't install dependency xfun (>= 0.18)
* xfun: Conflicts with xfun@0.53
* hunspell@3.0.6: dependency conflict
* jsonlite@2.0.0: dependency conflict
* jsonvalidate@1.5.0: dependency conflict
* knitr@1.50: Can't install dependency xfun (>= 0.51)
* rprojroot@2.1.1: dependency conflict
* spelling@2.3.2: Can't install dependency knitr
* stringi@1.8.7: dependency conflict
* styler@1.11.0: dependency conflict
* vctrs@0.6.5: dependency conflict
* stringr@1.5.2: dependency conflict
* callr@3.7.6: dependency conflict
* commonmark@2.0.0: dependency conflict
* cpp11@0.5.2: dependency conflict
* curl@7.0.0: dependency conflict
* desc@1.4.3: dependency conflict
* docopt@0.7.2: dependency conflict
* xmlparsedata@1.0.5: dependency conflict
* yaml@2.3.10: dependency conflict
* brew@1.0-10: dependency conflict
* evaluate@1.0.5: dependency conflict
* fs@1.6.6: dependency conflict
* glue@1.8.0: dependency conflict
* withr@3.0.2: dependency conflict
* xml2@1.4.1: dependency conflict
* lazyeval@0.2.2: dependency conflict
* lifecycle@1.0.4: dependency conflict
* lintr@3.2.0: Can't install dependency knitr
* rex@1.2.1: dependency conflict
* rlang@1.1.6: dependency conflict
* roxygen2@7.3.3: Can't install dependency knitr
* magrittr@2.0.4: dependency conflict
* pkgload@1.4.1: dependency conflict
* pkgbuild@1.4.8: dependency conflict
* processx@3.8.6: dependency conflict
* ps@1.9.1: dependency conflict
* purrr@1.1.0: dependency conflict
---
Backtrace:
1. renv::restore()
2. renv:::renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclu…
3. pak$pkg_install(pkg = remotes, ask = prompt)
4. pak:::remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...)…
5. err$throw(res$error)
---
Subprocess backtrace:
1. base::withCallingHandlers(cli_message = function(msg) { …
2. get("pkg_install_make_plan", asNamespace("pak"))(...)
3. prop$stop_for_solution_error()
4. private$plan$stop_for_solve_error()
5. pkgdepends:::pkgplan_stop_for_solve_error(self, private)
6. base::throw(new_error("Could not solve package dependencies:\n", msg, …
7. | base::signalCondition(cond)
8. global (function (e) …
Execution halted

Check the log at C:\Users\name.cache\pre-commit\pre-commit.log

Expected behavior
That precommit works.

Additional context

• My operating system is: Windows 11
• My project uses {renv}.
• the output of packageVersion('renv') 1.1.5

[lorenzwalthert]

Thanks. First, I see you overrode the default and probably set renv.config.pak.enabled to use {pak}. Can you check if the error also occurs with {pak} disabled?

Secondly, I don’t know which package conflicts with xfun@0.53. seems like {xfun} itself depends on {pak} and a new version was recently released.

[BjarkeHautop]

Thanks! Changing back to the default: RENV_CONFIG_PAK_ENABLED=FALSE fixes the issue.

[lorenzwalthert]

This most likely means that {renv} has not such an exact / picky dependency resolution mechanism as {pak} 😀. We should make it work with {pak} too.

[lorenzwalthert]

Let's wait for the next hook dependency update and see if using the latest {xfun} release helps...