diff --git a/.gitignore b/.gitignore
index 5131e198399a..803e0e6d8363 100644
--- a/.gitignore
+++ b/.gitignore
@@ -92,3 +92,7 @@ metastore_db
 
 plugin/updater_gpu/test/cpp/data
 /include/xgboost/build_config.h
+
+# files from R-package source install
+**/config.status
+R-package/src/Makevars