Installation fails only within isolated precommit environmnt
**Before filing a bug**
- [x] I have installed the latest dev version of {precommit} with `remotes::install_github('lorenzwalthert/precommit')`
- [x] I have installed the latest hook revisions (update with `precommit::autoupdate()`)
- [x] I have installed the latest release of the upstream Python framework pre-comit as described under the [update instructions](https://lorenzwalthert.github.io/precommit/dev/articles/precommit.html#update).
**stringi generates error when installing hooks**
I am trying to use the `style-files` and `lintr` hooks, which I have used in the past successfully many times (on previous machines). However, the installation breaks because I encounter errors when installing `{stringi}`. It seems to be an initial within the C++ compilers, however, my comparison of logs between running `install.packages("stringi")` successfully and the `{renv}` logs shows no difference in the identified compilers or commands.
Below is how I can reproduce it. Strangely, I can reproduce this directly on a UTM virtual machine, so is not unique to my machine, and myabe has something to do with my installation setup of `llvm` and `gcc`?
**To Reproduce**
Minimal yaml:
```yaml
repos:
- repo: https://github.com/lorenzwalthert/precommit
rev: v0.4.3.9008
hooks:
- id: style-files
- id: lintr
```
I have setup `pre-commit` using `uv add pre-commit` and then running `uv run pre-commit install --install-hooks`. This is the truncated log:
```
pre-commit version: 4.2.0
git --version: git version 2.49.0
sys.version:
3.13.1 (main, Dec 6 2024, 20:13:21) [Clang 18.1.8 ]
sys.executable: /Users/seth.caldwell/repos/r_test/.venv/bin/python
os.name: posix
sys.platform: darwin
** using staged installation
checking for R_HOME... /opt/homebrew/Cellar/r/4.5.1/lib/R
checking for R... /opt/homebrew/Cellar/r/4.5.1/lib/R/bin/R
checking for endianness... little
checking for cat... /bin/cat
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
accepts -g... yes
checking for /opt/homebrew/opt/llvm/bin/clang++ option to enable C++11 features... none needed
checking whether the C++ compiler supports the 'long long' type... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler supports the Standard Template Library... yes
checking whether std::map is available... yes
checking for pkg-config... /opt/homebrew/bin/pkg-config
checking with 'pkg-config' for the system ICU4C (icu-i18n icu-uc)... no
*** pkg-config did not detect ICU4C-devel libraries installed
*** Trying with 'standard' fallback flags
checking whether an ICU4C-based project can be built... no
*** This version of ICU4C cannot be used.
*** Using the ICU 74 bundle that comes with 'stringi'.
checking whether we may compile src/icu74/common/putil.cpp... yes
checking whether we may compile src/icu74/i18n/number_affixutils.cpp... yes
checking whether alignof(std::max_align_t) is available... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for elf.h... no
checking whether the ICU data library is available... icu74/data/icudt74l.dat.xz exists
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/uconfig_local.h
config.status: creating src/install.libs.R
*** stringi configure summary:
ICU_FOUND=0
ICUDT_DIR=icu74/data
ICU_BUNDLE_VERSION=74
ICUDT_ENDIANNESS=little
STRINGI_CXXSTD=
STRINGI_CXXFLAGS= -fPIC
STRINGI_CPPFLAGS=-I. -UDEBUG -DNDEBUG -Iicu74 -Iicu74/unicode -Iicu74/common -Iicu74/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -D_REENTRANT -DUCONFIG_USE_LOCAL
STRINGI_LDFLAGS=
STRINGI_LIBS=
*** Compiler settings used:
CXX=/opt/homebrew/opt/llvm/bin/clang++
LD=/opt/homebrew/opt/llvm/bin/clang++
CXXFLAGS=-g -O2
CPPFLAGS=-isystem /opt/homebrew/opt/llvm/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/opt/homebrew/opt/gettext/include
LDFLAGS=
LIBS=
** libs
using C++ compiler: ‘Homebrew clang version 20.1.7’
using SDK: ‘MacOSX15.4.sdk’
/opt/homebrew/opt/llvm/bin/clang++ -I"/opt/homebrew/Cellar/r/4.5.1/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -Iicu74 -Iicu74/unicode -Iicu74/common -Iicu74/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -D_REENTRANT -DUCONFIG_USE_LOCAL -isystem "/opt/homebrew/opt/llvm/include" -isysroot "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" -I"/opt/homebrew/opt/gettext/include" -fPIC -fPIC -g -O2 -c stri_brkiter.cpp -o stri_brkiter.o
In file included from stri_brkiter.cpp:32:
In file included from ./stri_stringi.h:36:
In file included from ./stri_external.h:68:
In file included from /opt/homebrew/Cellar/r/4.5.1/lib/R/include/R.h:70:
/opt/homebrew/Cellar/r/4.5.1/lib/R/include/R_ext/Boolean.h:62:36: warning: unknown warning group '-Wfixed-enum-extension', ignored [-Wunknown-warning-option]
62 | # pragma clang diagnostic ignored "-Wfixed-enum-extension"
| ^
In file included from stri_brkiter.cpp:32:
In file included from ./stri_stringi.h:36:
In file included from ./stri_external.h:68:
In file included from /opt/homebrew/Cellar/r/4.5.1/lib/R/include/R.h:73:
/opt/homebrew/Cellar/r/4.5.1/lib/R/include/R_ext/Error.h:58:3: error: 'noreturn' attribute does not appear on the first declaration
58 | [[noreturn]] void Rf_error(const char *, ...) R_PRINTF_FORMAT(1, 2);
| ^
./uconfig_local.h:55:23: note: previous declaration is here
55 | extern "C" void NORET Rf_error(const char *, ...);
| ^
1 warning and 1 error generated.
make: *** [stri_brkiter.o] Error 1
ERROR: compilation failed for package ‘stringi’
```
And here is the successful log from running `install.packages("stringi")`. I can also successfully run `renv::install("stringi")` if necessary, but haven't logged that (can if helpful).
```
* installing *source* package ‘stringi’ ...
** this is package ‘stringi’ version ‘1.8.7’
** package ‘stringi’ successfully unpacked and MD5 sums checked
** using staged installation
checking for R_HOME... /opt/homebrew/Cellar/r/4.5.1/lib/R
checking for R... /opt/homebrew/Cellar/r/4.5.1/lib/R/bin/R
checking for endianness... little
checking for cat... /bin/cat
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether /opt/homebrew/opt/llvm/bin/clang++ accepts -g... yes
checking for /opt/homebrew/opt/llvm/bin/clang++ option to enable C++11 features... none needed
checking whether the C++ compiler supports the 'long long' type... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler supports the Standard Template Library... yes
checking whether std::map is available... yes
checking for pkg-config... /opt/homebrew/bin/pkg-config
checking with 'pkg-config' for the system ICU4C (icu-i18n icu-uc)... no
*** pkg-config did not detect ICU4C-devel libraries installed
*** Trying with 'standard' fallback flags
checking whether an ICU4C-based project can be built... no
*** This version of ICU4C cannot be used.
*** Using the ICU 74 bundle that comes with 'stringi'.
checking whether we may compile src/icu74/common/putil.cpp... yes
checking whether we may compile src/icu74/i18n/number_affixutils.cpp... yes
checking whether alignof(std::max_align_t) is available... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for elf.h... no
checking whether the ICU data library is available... icu74/data/icudt74l.dat.xz exists
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/uconfig_local.h
config.status: creating src/install.libs.R
*** stringi configure summary:
ICU_FOUND=0
ICUDT_DIR=icu74/data
ICU_BUNDLE_VERSION=74
ICUDT_ENDIANNESS=little
STRINGI_CXXSTD=
STRINGI_CXXFLAGS= -fPIC
STRINGI_CPPFLAGS=-I. -UDEBUG -DNDEBUG -Iicu74 -Iicu74/unicode -Iicu74/common -Iicu74/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -D_REENTRANT -DUCONFIG_USE_LOCAL
STRINGI_LDFLAGS=
STRINGI_LIBS=
*** Compiler settings used:
CXX=/opt/homebrew/opt/llvm/bin/clang++
LD=/opt/homebrew/opt/llvm/bin/clang++
CXXFLAGS=-g -O2
CPPFLAGS=-isystem /opt/homebrew/opt/llvm/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/opt/homebrew/opt/gettext/include
LDFLAGS=
LIBS=
** libs
using C++ compiler: ‘Homebrew clang version 20.1.7’
using SDK: ‘MacOSX15.4.sdk’
/opt/homebrew/opt/llvm/bin/clang++ -I"/opt/homebrew/Cellar/r/4.5.1/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -Iicu74 -Iicu74/unicode -Iicu74/common -Iicu74/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -D_REENTRANT -DUCONFIG_USE_LOCAL -isystem "/opt/homebrew/opt/llvm/include" -isysroot "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" -I"/opt/homebrew/opt/gettext/include" -fPIC -fPIC -g -O2 -c stri_brkiter.cpp -o stri_brkiter.o
In file included from stri_brkiter.cpp:32:
In file included from ./stri_stringi.h:36:
In file included from ./stri_external.h:68:
In file included from /opt/homebrew/Cellar/r/4.5.1/lib/R/include/R.h:70:
/opt/homebrew/Cellar/r/4.5.1/lib/R/include/R_ext/Boolean.h:62:36: warning: unknown warning group '-Wfixed-enum-extension', ignored [-Wunknown-warning-option]
62 | # pragma clang diagnostic ignored "-Wfixed-enum-extension"
| ^
1 warning generated.
```
**Expected behavior**
I would expect this to work, as the C++ compilers are identical and clearly pulling from my `~/.R/Makevars`. But my guess is that something happens within `pre-commit` that I don't understand.
**Additional context**
- Here is `my sessionInfo()` that gives some platform information:
```
R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin24.4.0
Running under: macOS Sequoia 15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /opt/homebrew/Cellar/r/4.5.1/lib/R/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.5.1 tools_4.5.1 rstudioapi_0.17.1
```
Here is my `~/.R/Makevars`:
```
XCBASE:=$(shell xcrun --show-sdk-path)
LLVMBASE:=$(shell brew --prefix llvm)
GCCBASE:=$(shell brew --prefix gcc)
GETTEXT:=$(shell brew --prefix gettext)
CC=$(LLVMBASE)/bin/clang
CXX=$(LLVMBASE)/bin/clang++
CXX11=$(LLVMBASE)/bin/clang++
CXX14=$(LLVMBASE)/bin/clang++
CXX17=$(LLVMBASE)/bin/clang++
CXX1X=$(LLVMBASE)/bin/clang++
CPPFLAGS=-isystem "$(LLVMBASE)/include" -isysroot "$(XCBASE)" -I"$(GETTEXT)/include"
LDFLAGS=-L"$(LLVMBASE)/lib" -lomp -L"$(GETTEXT)/lib" --sysroot="$(XCBASE)"
FC=$(GCCBASE)/bin/gfortran
F77=$(GCCBASE)/bin/gfortran
FLIBS=-L$(GCCBASE)/lib/gcc/9/ -lm
```
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