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Posted to issues@arrow.apache.org by "WillAyd (via GitHub)" <gi...@apache.org> on 2025/10/29 20:57:30 UTC
[I] pre-commit RScript local check fails on ubuntu 25.10 [arrow]
WillAyd opened a new issue, #47997:
URL: https://github.com/apache/arrow/issues/47997
### Describe the bug, including details regarding any error messages, version, and platform.
I get the following error when trying to run pre-commit on ubuntu 25.10:
<details>
```
pre-commit version: 4.2.0
git --version: git version 2.51.0
sys.version:
3.13.7 (main, Aug 20 2025, 22:17:40) [GCC 15.2.0]
sys.executable: /usr/bin/python3
os.name: posix
sys.platform: linux
```
### error information
```
An unexpected error has occurred: CalledProcessError: command: ('/usr/bin/Rscript', '--no-save', '--no-restore', '--no-site-file', '--no-environ', '/tmp/tmp_40_6sb2/script.R', 'cyclocomp', 'lintr', 'testthat')
return code: 1
stdout:
Retrieving 'https://cran.rstudio.com/src/contrib/lintr_3.2.0.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/xml2_1.4.1.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/xmlparsedata_1.0.5.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/testthat_3.2.3.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/brio_1.1.5.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/jsonlite_2.0.0.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/lifecycle_1.0.4.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/magrittr_2.0.4.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/pkgload_1.4.1.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/fs_1.6.6.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/pkgbuild_1.4.8.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/rprojroot_2.1.1.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/praise_1.0.0.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/waldo_0.6.2.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/diffobj_0.3.6.tar.gz' ...
OK [file is up to date]
Installing ps [1.9.1] ...
OK [linked cache]
Installing R6 [2.6.1] ...
OK [linked cache]
Installing processx [3.8.6] ...
OK [linked cache]
Installing callr [3.7.6] ...
OK [linked cache]
Installing crayon [1.5.3] ...
OK [linked cache]
Installing cli [3.6.5] ...
OK [linked cache]
Installing desc [1.4.3] ...
OK [linked cache]
Installing remotes [2.5.0] ...
OK [linked cache]
Installing withr [3.0.2] ...
OK [linked cache]
Installing cyclocomp [1.1.1] ...
OK [linked cache]
Installing backports [1.5.0] ...
OK [linked cache]
Installing digest [0.6.37] ...
OK [linked cache]
Installing glue [1.8.0] ...
OK [linked cache]
Installing evaluate [1.0.5] ...
OK [linked cache]
Installing xfun [0.53] ...
OK [linked cache]
Installing highr [0.11] ...
OK [linked cache]
Installing yaml [2.3.10] ...
OK [linked cache]
Installing knitr [1.50] ...
OK [linked cache]
Installing lazyeval [0.2.2] ...
OK [linked cache]
Installing rex [1.2.1] ...
OK [linked cache]
Installing rlang [1.1.6] ...
OK [linked cache]
Installing xml2 [1.4.1] ...
FAILED
Error installing package 'xml2':
================================
* installing to library ‘/tmp/RtmpWEOOb1/renv-staging-418702fde9c’
* installing *source* package ‘xml2’ ...
** this is package ‘xml2’ version ‘1.4.1’
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include
Using PKG_LIBS=-L/home/will/miniforge3/envs/shimano-dev/lib -lxml2 -L/home/will/miniforge3/envs/shimano-dev/lib -lz -L/home/will/miniforge3/envs/shimano-dev/lib -llzma -L/home/will/miniforge3/envs/shimano-dev/lib -licui18n -licuuc -licudata -L/home/will/miniforge3/envs/shimano-dev/lib -liconv -lm -ldl
** libs
using C compiler: ‘gcc (Ubuntu 15.2.0-4ubuntu4) 15.2.0’
using C++ compiler: ‘g++ (Ubuntu 15.2.0-4ubuntu4) 15.2.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c connection.cpp -o connection.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_doc.cpp -o xml2_doc.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_init.c -o xml2_init.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_namespace.cpp -o xml2_namespace.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_node.cpp -o xml2_node.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_output.cpp -o xml2_output.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_schema.cpp -o xml2_schema.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_url.cpp -o xml2_url.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_xpath.cpp -o xml2_xpath.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o xml2.so connection.o init.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -L/home/will/miniforge3/envs/shimano-dev/lib -lxml2 -L/home/will/miniforge3/envs/shimano-dev/lib -lz -L/home/will/miniforge3/envs/shimano-dev/lib -llzma -L/home/will/miniforge3/envs/shimano-dev/lib -licui18n -licuuc -licudata -L/home/will/miniforge3/envs/shimano-dev/lib -liconv -lm -ldl -L/usr/lib/R/lib -lR
installing to /tmp/RtmpWEOOb1/renv-staging-418702fde9c/00LOCK-xml2/00new/xml2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘xml2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/tmp/RtmpWEOOb1/renv-staging-418702fde9c/00LOCK-xml2/00new/xml2/libs/xml2.so':
libxml2.so.2: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/tmp/RtmpWEOOb1/renv-staging-418702fde9c/xml2’
stderr:
Error: install of package 'xml2' failed
Traceback (most recent calls last):
12: renv::install(commandArgs(trailingOnly = TRUE))
11: renv_install(records)
10: renv_install_staged(records)
9: renv_install_default(records)
8: handler(package, renv_install_impl(record))
7: renv_install_impl(record)
6: withCallingHandlers(renv_install_package_local(record), error = function(e) {
vwritef("\tFAILED")
writef(e$output)
})
5: renv_install_package_local(record)
4: renv_install_package_local_impl(package, path)
3: r_cmd_install(package, path)
2: r_exec_error(package, output, "install")
1: stop(error)
Execution halted
```
```
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/pre_commit/error_handler.py", line 73, in error_handler
yield
File "/usr/lib/python3/dist-packages/pre_commit/main.py", line 389, in main
return hook_impl(
store,
...<5 lines>...
args=args.rest[1:],
)
File "/usr/lib/python3/dist-packages/pre_commit/commands/hook_impl.py", line 271, in hook_impl
return retv | run(config, store, ns)
~~~^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pre_commit/commands/run.py", line 442, in run
install_hook_envs(to_install, store)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pre_commit/repository.py", line 229, in install_hook_envs
_hook_install(hook)
~~~~~~~~~~~~~^^^^^^
File "/usr/lib/python3/dist-packages/pre_commit/repository.py", line 85, in _hook_install
lang.install_environment(
~~~~~~~~~~~~~~~~~~~~~~~~^
hook.prefix, hook.language_version, hook.additional_dependencies,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/usr/lib/python3/dist-packages/pre_commit/languages/r.py", line 238, in install_environment
_execute_r_in_renv(
~~~~~~~~~~~~~~~~~~^
code=r_code_inst_add, prefix=prefix, version=version,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
args=additional_dependencies,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=env_dir,
^^^^^^^^^^^^
)
^
File "/usr/lib/python3/dist-packages/pre_commit/languages/r.py", line 44, in _execute_r_in_renv
return _execute_r(
code=code, prefix=prefix, version=version, args=args, cwd=cwd,
cli_opts=_RENV_ACTIVATED_OPTS,
)
File "/usr/lib/python3/dist-packages/pre_commit/languages/r.py", line 34, in _execute_r
_, out, _ = cmd_output(
~~~~~~~~~~^
_rscript_exec(), *cli_opts, f, *args, cwd=cwd,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/usr/lib/python3/dist-packages/pre_commit/util.py", line 117, in cmd_output
returncode, stdout_b, stderr_b = cmd_output_b(*cmd, **kwargs)
~~~~~~~~~~~~^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pre_commit/util.py", line 111, in cmd_output_b
raise CalledProcessError(returncode, cmd, stdout_b, stderr_b)
pre_commit.util.CalledProcessError: command: ('/usr/bin/Rscript', '--no-save', '--no-restore', '--no-site-file', '--no-environ', '/tmp/tmp_40_6sb2/script.R', 'cyclocomp', 'lintr', 'testthat')
return code: 1
stdout:
Retrieving 'https://cran.rstudio.com/src/contrib/lintr_3.2.0.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/xml2_1.4.1.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/xmlparsedata_1.0.5.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/testthat_3.2.3.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/brio_1.1.5.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/jsonlite_2.0.0.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/lifecycle_1.0.4.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/magrittr_2.0.4.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/pkgload_1.4.1.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/fs_1.6.6.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/pkgbuild_1.4.8.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/rprojroot_2.1.1.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/praise_1.0.0.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/waldo_0.6.2.tar.gz' ...
OK [file is up to date]
Retrieving 'https://cran.rstudio.com/src/contrib/diffobj_0.3.6.tar.gz' ...
OK [file is up to date]
Installing ps [1.9.1] ...
OK [linked cache]
Installing R6 [2.6.1] ...
OK [linked cache]
Installing processx [3.8.6] ...
OK [linked cache]
Installing callr [3.7.6] ...
OK [linked cache]
Installing crayon [1.5.3] ...
OK [linked cache]
Installing cli [3.6.5] ...
OK [linked cache]
Installing desc [1.4.3] ...
OK [linked cache]
Installing remotes [2.5.0] ...
OK [linked cache]
Installing withr [3.0.2] ...
OK [linked cache]
Installing cyclocomp [1.1.1] ...
OK [linked cache]
Installing backports [1.5.0] ...
OK [linked cache]
Installing digest [0.6.37] ...
OK [linked cache]
Installing glue [1.8.0] ...
OK [linked cache]
Installing evaluate [1.0.5] ...
OK [linked cache]
Installing xfun [0.53] ...
OK [linked cache]
Installing highr [0.11] ...
OK [linked cache]
Installing yaml [2.3.10] ...
OK [linked cache]
Installing knitr [1.50] ...
OK [linked cache]
Installing lazyeval [0.2.2] ...
OK [linked cache]
Installing rex [1.2.1] ...
OK [linked cache]
Installing rlang [1.1.6] ...
OK [linked cache]
Installing xml2 [1.4.1] ...
FAILED
Error installing package 'xml2':
================================
* installing to library ‘/tmp/RtmpWEOOb1/renv-staging-418702fde9c’
* installing *source* package ‘xml2’ ...
** this is package ‘xml2’ version ‘1.4.1’
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include
Using PKG_LIBS=-L/home/will/miniforge3/envs/shimano-dev/lib -lxml2 -L/home/will/miniforge3/envs/shimano-dev/lib -lz -L/home/will/miniforge3/envs/shimano-dev/lib -llzma -L/home/will/miniforge3/envs/shimano-dev/lib -licui18n -licuuc -licudata -L/home/will/miniforge3/envs/shimano-dev/lib -liconv -lm -ldl
** libs
using C compiler: ‘gcc (Ubuntu 15.2.0-4ubuntu4) 15.2.0’
using C++ compiler: ‘g++ (Ubuntu 15.2.0-4ubuntu4) 15.2.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c connection.cpp -o connection.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_doc.cpp -o xml2_doc.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_init.c -o xml2_init.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_namespace.cpp -o xml2_namespace.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_node.cpp -o xml2_node.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_output.cpp -o xml2_output.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_schema.cpp -o xml2_schema.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_url.cpp -o xml2_url.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/home/will/miniforge3/envs/shimano-dev/include/libxml2 -I/home/will/miniforge3/envs/shimano-dev/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-9qMsDV/r-base-4.5.1=/usr/src/r-base-4.5.1-1 -Wdate-time -D_FORTIFY_SOURCE=3 -c xml2_xpath.cpp -o xml2_xpath.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o xml2.so connection.o init.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -L/home/will/miniforge3/envs/shimano-dev/lib -lxml2 -L/home/will/miniforge3/envs/shimano-dev/lib -lz -L/home/will/miniforge3/envs/shimano-dev/lib -llzma -L/home/will/miniforge3/envs/shimano-dev/lib -licui18n -licuuc -licudata -L/home/will/miniforge3/envs/shimano-dev/lib -liconv -lm -ldl -L/usr/lib/R/lib -lR
installing to /tmp/RtmpWEOOb1/renv-staging-418702fde9c/00LOCK-xml2/00new/xml2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘xml2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/tmp/RtmpWEOOb1/renv-staging-418702fde9c/00LOCK-xml2/00new/xml2/libs/xml2.so':
libxml2.so.2: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/tmp/RtmpWEOOb1/renv-staging-418702fde9c/xml2’
stderr:
Error: install of package 'xml2' failed
Traceback (most recent calls last):
12: renv::install(commandArgs(trailingOnly = TRUE))
11: renv_install(records)
10: renv_install_staged(records)
9: renv_install_default(records)
8: handler(package, renv_install_impl(record))
7: renv_install_impl(record)
6: withCallingHandlers(renv_install_package_local(record), error = function(e) {
vwritef("\tFAILED")
writef(e$output)
})
5: renv_install_package_local(record)
4: renv_install_package_local_impl(package, path)
3: r_cmd_install(package, path)
2: r_exec_error(package, output, "install")
1: stop(error)
Execution halted
```
</details>
This did not happen on Ubuntu 25.04. The libxml2-dev package is installed on my computer, if that matters
### Component(s)
R, Developer Tools
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Re: [I] [R][Dev] pre-commit RScript local check fails on ubuntu 25.10 [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #47997:
URL: https://github.com/apache/arrow/issues/47997#issuecomment-3925289464
I don't think there's anything we can do here; analysis from :robot: says "it's is a conflict between conda and pre-commit's R language support. When conda is active, pkg-config finds libxml2 from your conda environment `(/home/will/miniforge3/envs/shimano-dev/lib)`, but pre-commit's renv doesn't inherit `LD_LIBRARY_PATH`, so the compiled package can't load the library at runtime."
Looks like a consequence of having different needs for different languages with a single pre-commit hook. I'm guessing you got a workaround like only running whichever hooks instead of them all? Lmk
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Re: [I] [R][Dev] pre-commit RScript local check fails on ubuntu 25.10 [arrow]
Posted by "jorisvandenbossche (via GitHub)" <gi...@apache.org>.
jorisvandenbossche commented on issue #47997:
URL: https://github.com/apache/arrow/issues/47997#issuecomment-5773343240
I think this is essentially resolved by https://github.com/apache/arrow/pull/50851 as well (we no longer need an installed R, so it also won't fail with an R from conda)
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Re: [I] [R][Dev] pre-commit RScript local check fails on ubuntu 25.10 [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic closed issue #47997: [R][Dev] pre-commit RScript local check fails on ubuntu 25.10
URL: https://github.com/apache/arrow/issues/47997
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