[R-package] compiler warning on clang + arm64 macOS: argument unused during compilation: '-msse2'

[jameslamb]

Description

While testing the R package after it was switched from autoconf to CMake (#12416), I found that R CMD check --as-cran now raises 1 WARNING on Apple Silicon (e.g. my M2 macbook).

* checking whether package ‘xgboost’ can be installed ... [181s/183s] WARNING
Found the following significant warnings:
  clang: warning: argument unused during compilation: '-msse2' [-Wunused-command-line-argument]

That warning is harmless (it just means "you used an x86-specific flag on a non-x86 system"), but the fact that R CMD check --as-cran emits a WARNING could be enough to cause delays publishing to CRAN. It should be fixed if the fix isn't too much complexity.

Reproducible Example

$ git clean -dfX
$ python -B ops/script/test_r_package.py --task build
$ TEMP_DIR=$(mktemp -d)
$ cp ./xgboost_3.5.0.0.tar.gz "${TEMP_DIR}"/
$ pushd "${TEMP_DIR}"
$ R CMD check --as-cran ./xgboost*.tar.gz
* using R version 4.6.0 (2026-04-24)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* current time: 2026-08-20 03:35:09 UTC
* using option ‘--as-cran’
...
* checking whether package ‘xgboost’ can be installed ... [181s/183s] WARNING
Found the following significant warnings:
  clang: warning: argument unused during compilation: '-msse2' [-Wunused-command-line-argument]
See ‘/private/var/folders/6d/80svzp0d0z1dr414fgnvll6h0000gn/T/tmp.Q5X4NeFmeo/xgboost.Rcheck/00install.out’ for details.

Looks like that is coming from dmlc-core.

[  3%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/config.cc.o
clang: warning: argument unused during compilation: '-msse2' [-Wunused-command-line-argument]
[  4%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/data.cc.o
clang: warning: argument unused during compilation: '-msse2' [-Wunused-command-line-argument]
... etc., etc.

Notes

Why not just suppress it with a -Wno flag?

Suppressing warnings with -Wno-unused-command-line-argument is not allowed by the CRAN policies. From https://cran.r-project.org/web/packages/policies.html

Packages should not attempt to disable compiler diagnostics, nor to remove other diagnostic information such as symbols in shared objects.

XGBoost has been on CRAN and using dmlc-core for a long time, why would this only be a problem now?

I think the switch to CMake means dmlc-core's compiler flags are coming through from its CMake. I don't see this warning in the most recent CRAN checks for XGBoost on CRAN *(based on XGBoost 3.2.1.1):

• all checks: https://cran.r-project.org/web/checks/check_results_xgboost.html
• macOS arm64 build: https://www.r-project.org/nosvn/R.check/r-oldrel-macos-arm64/xgboost-00install.html

Approach

• fix in dmlc-core (prevent -msse2 from being omitted when targeting non-x86 platforms dmlc-core#722)
• update dmlc-core submodule here