pre-commit version: 4.6.0
git --version: git version 2.50.1 (Apple Git-155)
sys.version:
3.14.5 (main, May 10 2026, 10:21:34) [Clang 21.0.0 (clang-2100.0.123.102)]
sys.executable: /opt/homebrew/Cellar/pre-commit/4.6.0/libexec/bin/python3.14
os.name: posix
sys.platform: darwin
An unexpected error has occurred: CalledProcessError: command: ('/Library/Frameworks/R.framework/Resources/bin/Rscript', '--vanilla', '/var/folders/ss/6msy9pqs3556370vh8s084l80000gp/T/tmpa0ef6b36/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 updated:
# RSPM -----------------------------------------------------------------------
- backports [* -> 1.5.0]
- brew [* -> 1.0-10]
- callr [* -> 3.7.6]
- cli [* -> 3.6.5]
- commonmark [* -> 2.0.0]
- cpp11 [* -> 0.5.2]
- curl [* -> 7.0.0]
- desc [* -> 1.4.3]
- digest [* -> 0.6.39]
- docopt [* -> 0.7.2]
- evaluate [* -> 1.0.5]
- fs [* -> 1.6.6]
- glue [* -> 1.8.0]
- here [* -> 1.0.2]
- highr [* -> 0.11]
- hunspell [* -> 3.0.6]
- jsonlite [* -> 2.0.0]
- jsonvalidate [* -> 1.5.0]
- knitr [* -> 1.51]
- lazyeval [* -> 0.2.2]
- lifecycle [* -> 1.0.5]
- lintr [* -> 3.3.0-1]
- magrittr [* -> 2.0.4]
- pkgbuild [* -> 1.4.8]
- pkgload [* -> 1.4.1]
- processx [* -> 3.8.6]
- ps [* -> 1.9.1]
- purrr [* -> 1.2.1]
- R.cache [* -> 0.17.0]
- R.methodsS3 [* -> 1.8.2]
- R.oo [* -> 1.27.1]
- R.utils [* -> 2.13.0]
- R6 [* -> 2.6.1]
- Rcpp [* -> 1.1.1]
- rex [* -> 1.2.1]
- rlang [* -> 1.1.7]
- roxygen2 [* -> 7.3.3]
- rprojroot [* -> 2.1.1]
- spelling [* -> 2.3.2]
- stringi [* -> 1.8.7]
- stringr [* -> 1.6.0]
- styler [* -> 1.11.0]
- V8 [* -> 8.0.1]
- vctrs [* -> 0.6.5]
- withr [* -> 3.0.2]
- xfun [* -> 0.55]
- xml2 [* -> 1.5.1]
- xmlparsedata [* -> 1.0.5]
- yaml [* -> 2.3.12]
# Downloading packages -------------------------------------------------------
- Downloading Rcpp from RSPM ... OK [file is up to date]
- Downloading V8 from RSPM ... OK [file is up to date]
- Downloading jsonlite from RSPM ... OK [file is up to date]
- Downloading curl from RSPM ... OK [file is up to date]
- Downloading backports from RSPM ... OK [file is up to date]
- Downloading brew from RSPM ... OK [file is up to date]
- Downloading callr from RSPM ... OK [file is up to date]
- Downloading processx from RSPM ... OK [file is up to date]
- Downloading ps from RSPM ... OK [file is up to date]
- Downloading cli from RSPM ... OK [file is up to date]
- Downloading commonmark from RSPM ... OK [file is up to date]
- Downloading cpp11 from RSPM ... OK [file is up to date]
- Downloading desc from RSPM ... OK [file is up to date]
- Downloading docopt from RSPM ... OK [file is up to date]
- Downloading evaluate from RSPM ... OK [file is up to date]
- Downloading fs from RSPM ... OK [file is up to date]
- Downloading glue from RSPM ... OK [file is up to date]
- Downloading here from RSPM ... OK [file is up to date]
- Downloading rprojroot from RSPM ... OK [file is up to date]
- Downloading highr from RSPM ... OK [file is up to date]
- Downloading xfun from RSPM ... OK [file is up to date]
- Downloading hunspell from RSPM ... OK [file is up to date]
- Downloading jsonvalidate from RSPM ... OK [file is up to date]
- Downloading knitr from RSPM ... OK [file is up to date]
- Downloading yaml from RSPM ... OK [file is up to date]
- Downloading lazyeval from RSPM ... OK [file is up to date]
- Downloading lifecycle from RSPM ... OK [file is up to date]
- Downloading rlang from RSPM ... OK [file is up to date]
- Downloading lintr from RSPM ... OK [file is up to date]
- Downloading rex from RSPM ... OK [file is up to date]
- Downloading xml2 from RSPM ... OK [file is up to date]
- Downloading xmlparsedata from RSPM ... OK [file is up to date]
- Downloading magrittr from RSPM ... OK [file is up to date]
- Downloading pkgbuild from RSPM ... OK [file is up to date]
- Downloading pkgload from RSPM ... OK [file is up to date]
- Downloading purrr from RSPM ... OK [file is up to date]
- Downloading vctrs from RSPM ... OK [file is up to date]
- Downloading roxygen2 from RSPM ... OK [file is up to date]
- Downloading stringi from RSPM ... OK [file is up to date]
- Downloading stringr from RSPM ... OK [file is up to date]
- Downloading withr from RSPM ... OK [file is up to date]
- Downloading spelling from RSPM ... OK [file is up to date]
- Downloading styler from RSPM ... OK [file is up to date]
Successfully downloaded 43 packages in 17 seconds.
# Installing packages --------------------------------------------------------
- Installing R.methodsS3 ... OK [linked from cache]
- Installing R.oo ... OK [linked from cache]
- Installing R.utils ... OK [linked from cache]
- Installing digest ... OK [linked from cache]
- Installing R.cache ... OK [linked from cache]
- Installing R6 ... OK [linked from cache]
- Installing Rcpp ... FAILED
Traceback (most recent calls last):
13: renv::restore()
12: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
11: renv_install_impl(records)
10: renv_install_staged(records)
9: renv_install_default(records)
8: handler(package, renv_install_package(record))
7: renv_install_package(record)
6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
5: renv_install_package_impl(record)
4: r_cmd_install(package, path)
3: r_exec_error(package, output, "install", status)
2: abort(all)
1: stop(fallback)
stderr:
Error: Error installing package 'Rcpp':
================================
* installing *source* package ‘Rcpp’ ...
** this is package ‘Rcpp’ version ‘1.1.1’
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
Warning: running 'cleanup' failed
** libs
using C++ compiler: ‘Apple clang version 21.0.0 (clang-2100.0.123.102)’
using SDK: ‘MacOSX26.4.1.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c api.cpp -o api.o
In file included from api.cpp:26:
In file included from ../inst/include/Rcpp.h:49:
../inst/include/Rcpp/Function.h:75:65: error: use of undeclared identifier 'R_NamespaceRegistry'
75 | Shield<SEXP> env(R_getVarEx(Rf_install(ns.c_str()), R_NamespaceRegistry, FALSE, R_UnboundValue));
| ^~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [api.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/Users/pschloss/.cache/pre-commit/reposinjmr3q/renv-default/renv/staging/1/Rcpp’
install of package 'Rcpp' failed [error code 1]
Execution halted
Traceback (most recent call last):
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/error_handler.py", line 73, in error_handler
yield
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/main.py", line 401, in main
return hook_impl(
store,
...<5 lines>...
args=args.rest[1:],
)
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/commands/hook_impl.py", line 275, in hook_impl
return retv | run(config, store, ns)
~~~^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/commands/run.py", line 443, in run
install_hook_envs(to_install, store)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/repository.py", line 229, in install_hook_envs
_hook_install(hook)
~~~~~~~~~~~~~^^^^^^
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/repository.py", line 85, in _hook_install
lang.install_environment(
~~~~~~~~~~~~~~~~~~~~~~~~^
hook.prefix, hook.language_version, hook.additional_dependencies,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/languages/r.py", line 230, in install_environment
_execute_vanilla_r(
~~~~~~~~~~~~~~~~~~^
r_code_inst_environment,
^^^^^^^^^^^^^^^^^^^^^^^^
prefix=prefix, version=version, cwd=env_dir,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/languages/r.py", line 54, in _execute_vanilla_r
return _execute_r(
code=code, prefix=prefix, version=version, args=args, cwd=cwd,
cli_opts=('--vanilla',),
)
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/languages/r.py", line 34, in _execute_r
_, out, _ = cmd_output(
~~~~~~~~~~^
_rscript_exec(), *cli_opts, f, *args, cwd=cwd,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/util.py", line 117, in cmd_output
returncode, stdout_b, stderr_b = cmd_output_b(*cmd, **kwargs)
~~~~~~~~~~~~^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/pre-commit/4.6.0/libexec/lib/python3.14/site-packages/pre_commit/util.py", line 111, in cmd_output_b
raise CalledProcessError(returncode, cmd, stdout_b, stderr_b)
pre_commit.util.CalledProcessError: command: ('/Library/Frameworks/R.framework/Resources/bin/Rscript', '--vanilla', '/var/folders/ss/6msy9pqs3556370vh8s084l80000gp/T/tmpa0ef6b36/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 updated:
# RSPM -----------------------------------------------------------------------
- backports [* -> 1.5.0]
- brew [* -> 1.0-10]
- callr [* -> 3.7.6]
- cli [* -> 3.6.5]
- commonmark [* -> 2.0.0]
- cpp11 [* -> 0.5.2]
- curl [* -> 7.0.0]
- desc [* -> 1.4.3]
- digest [* -> 0.6.39]
- docopt [* -> 0.7.2]
- evaluate [* -> 1.0.5]
- fs [* -> 1.6.6]
- glue [* -> 1.8.0]
- here [* -> 1.0.2]
- highr [* -> 0.11]
- hunspell [* -> 3.0.6]
- jsonlite [* -> 2.0.0]
- jsonvalidate [* -> 1.5.0]
- knitr [* -> 1.51]
- lazyeval [* -> 0.2.2]
- lifecycle [* -> 1.0.5]
- lintr [* -> 3.3.0-1]
- magrittr [* -> 2.0.4]
- pkgbuild [* -> 1.4.8]
- pkgload [* -> 1.4.1]
- processx [* -> 3.8.6]
- ps [* -> 1.9.1]
- purrr [* -> 1.2.1]
- R.cache [* -> 0.17.0]
- R.methodsS3 [* -> 1.8.2]
- R.oo [* -> 1.27.1]
- R.utils [* -> 2.13.0]
- R6 [* -> 2.6.1]
- Rcpp [* -> 1.1.1]
- rex [* -> 1.2.1]
- rlang [* -> 1.1.7]
- roxygen2 [* -> 7.3.3]
- rprojroot [* -> 2.1.1]
- spelling [* -> 2.3.2]
- stringi [* -> 1.8.7]
- stringr [* -> 1.6.0]
- styler [* -> 1.11.0]
- V8 [* -> 8.0.1]
- vctrs [* -> 0.6.5]
- withr [* -> 3.0.2]
- xfun [* -> 0.55]
- xml2 [* -> 1.5.1]
- xmlparsedata [* -> 1.0.5]
- yaml [* -> 2.3.12]
# Downloading packages -------------------------------------------------------
- Downloading Rcpp from RSPM ... OK [file is up to date]
- Downloading V8 from RSPM ... OK [file is up to date]
- Downloading jsonlite from RSPM ... OK [file is up to date]
- Downloading curl from RSPM ... OK [file is up to date]
- Downloading backports from RSPM ... OK [file is up to date]
- Downloading brew from RSPM ... OK [file is up to date]
- Downloading callr from RSPM ... OK [file is up to date]
- Downloading processx from RSPM ... OK [file is up to date]
- Downloading ps from RSPM ... OK [file is up to date]
- Downloading cli from RSPM ... OK [file is up to date]
- Downloading commonmark from RSPM ... OK [file is up to date]
- Downloading cpp11 from RSPM ... OK [file is up to date]
- Downloading desc from RSPM ... OK [file is up to date]
- Downloading docopt from RSPM ... OK [file is up to date]
- Downloading evaluate from RSPM ... OK [file is up to date]
- Downloading fs from RSPM ... OK [file is up to date]
- Downloading glue from RSPM ... OK [file is up to date]
- Downloading here from RSPM ... OK [file is up to date]
- Downloading rprojroot from RSPM ... OK [file is up to date]
- Downloading highr from RSPM ... OK [file is up to date]
- Downloading xfun from RSPM ... OK [file is up to date]
- Downloading hunspell from RSPM ... OK [file is up to date]
- Downloading jsonvalidate from RSPM ... OK [file is up to date]
- Downloading knitr from RSPM ... OK [file is up to date]
- Downloading yaml from RSPM ... OK [file is up to date]
- Downloading lazyeval from RSPM ... OK [file is up to date]
- Downloading lifecycle from RSPM ... OK [file is up to date]
- Downloading rlang from RSPM ... OK [file is up to date]
- Downloading lintr from RSPM ... OK [file is up to date]
- Downloading rex from RSPM ... OK [file is up to date]
- Downloading xml2 from RSPM ... OK [file is up to date]
- Downloading xmlparsedata from RSPM ... OK [file is up to date]
- Downloading magrittr from RSPM ... OK [file is up to date]
- Downloading pkgbuild from RSPM ... OK [file is up to date]
- Downloading pkgload from RSPM ... OK [file is up to date]
- Downloading purrr from RSPM ... OK [file is up to date]
- Downloading vctrs from RSPM ... OK [file is up to date]
- Downloading roxygen2 from RSPM ... OK [file is up to date]
- Downloading stringi from RSPM ... OK [file is up to date]
- Downloading stringr from RSPM ... OK [file is up to date]
- Downloading withr from RSPM ... OK [file is up to date]
- Downloading spelling from RSPM ... OK [file is up to date]
- Downloading styler from RSPM ... OK [file is up to date]
Successfully downloaded 43 packages in 17 seconds.
# Installing packages --------------------------------------------------------
- Installing R.methodsS3 ... OK [linked from cache]
- Installing R.oo ... OK [linked from cache]
- Installing R.utils ... OK [linked from cache]
- Installing digest ... OK [linked from cache]
- Installing R.cache ... OK [linked from cache]
- Installing R6 ... OK [linked from cache]
- Installing Rcpp ... FAILED
Traceback (most recent calls last):
13: renv::restore()
12: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
11: renv_install_impl(records)
10: renv_install_staged(records)
9: renv_install_default(records)
8: handler(package, renv_install_package(record))
7: renv_install_package(record)
6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
5: renv_install_package_impl(record)
4: r_cmd_install(package, path)
3: r_exec_error(package, output, "install", status)
2: abort(all)
1: stop(fallback)
stderr:
Error: Error installing package 'Rcpp':
================================
* installing *source* package ‘Rcpp’ ...
** this is package ‘Rcpp’ version ‘1.1.1’
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
Warning: running 'cleanup' failed
** libs
using C++ compiler: ‘Apple clang version 21.0.0 (clang-2100.0.123.102)’
using SDK: ‘MacOSX26.4.1.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c api.cpp -o api.o
In file included from api.cpp:26:
In file included from ../inst/include/Rcpp.h:49:
../inst/include/Rcpp/Function.h:75:65: error: use of undeclared identifier 'R_NamespaceRegistry'
75 | Shield<SEXP> env(R_getVarEx(Rf_install(ns.c_str()), R_NamespaceRegistry, FALSE, R_UnboundValue));
| ^~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [api.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/Users/pschloss/.cache/pre-commit/reposinjmr3q/renv-default/renv/staging/1/Rcpp’
install of package 'Rcpp' failed [error code 1]
Execution halted
Before filing a bug
remotes::install_github('lorenzwalthert/precommit')precommit::autoupdate())Describe the bug
Additional context
Perhaps related to #616. Also possibly related to RcppCore/Rcpp#1473? If that's the case, is there a way to have precommit install Rcpp from github rather than CRAN?
cat .cache/pre-commit/pre-commit.log
version information
error information