diff --git a/R-package/configure b/R-package/configure
index 02fcfa028b0d..f75666297982 100755
--- a/R-package/configure
+++ b/R-package/configure
@@ -1694,9 +1694,6 @@ if test -z "${R_HOME}"; then
     exit 1
 fi
 CC=`"${R_HOME}/bin/R" CMD config CC`
-CXX=`"${R_HOME}/bin/R" CMD config CXX11`
-CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
-CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 
 # LightGBM-specific flags
 LGB_CPPFLAGS=""
diff --git a/R-package/configure.ac b/R-package/configure.ac
index 20182666b502..4dfa2c43c09a 100644
--- a/R-package/configure.ac
+++ b/R-package/configure.ac
@@ -21,9 +21,6 @@ if test -z "${R_HOME}"; then
     exit 1
 fi
 CC=`"${R_HOME}/bin/R" CMD config CC`
-CXX=`"${R_HOME}/bin/R" CMD config CXX11`
-CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
-CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 
 # LightGBM-specific flags
 LGB_CPPFLAGS=""