diff --git a/configure b/configure
index ede3910..76bbc64 100755
--- a/configure
+++ b/configure
@@ -5,7 +5,7 @@ RCPP_PARALLEL_CPPFLAGS=`"${R_HOME}/bin/Rscript" -e "cat(RcppParallel::CxxFlags()
 RCPP_PARALLEL_LIBS=`"${R_HOME}/bin/Rscript" -e "cat(RcppParallel::LdFlags())"`
 
 # Generate sources.mk using R
-"${R_HOME}/bin/Rscript" R/generate_makevars_sources.R > src/sources.mk
+"${R_HOME}/bin/Rscript" inst/generate_makevars_sources.R > src/sources.mk
 
 # Substitute into Makevars
 sed -e "s|@RCPP_PARALLEL_CPPFLAGS@|${RCPP_PARALLEL_CPPFLAGS}|" \
diff --git a/configure.win b/configure.win
index 01a338b..794af7a 100755
--- a/configure.win
+++ b/configure.win
@@ -5,7 +5,7 @@ RCPP_PARALLEL_CPPFLAGS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "cat(RcppPar
 RCPP_PARALLEL_LIBS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "cat(RcppParallel::LdFlags())"`
 
 # Generate sources.mk using R
-"${R_HOME}/bin/Rscript" R/generate_makevars_sources.R > src/sources.mk
+"${R_HOME}/bin/Rscript" inst/generate_makevars_sources.R > src/sources.mk
 
 # Substitute into Makevars.win
 sed -e "s|@RCPP_PARALLEL_CPPFLAGS@|${RCPP_PARALLEL_CPPFLAGS}|" \
diff --git a/R/generate_makevars_sources.R b/inst/generate_makevars_sources.R
similarity index 75%
rename from R/generate_makevars_sources.R
rename to inst/generate_makevars_sources.R
index 4662476..cb238c4 100644
--- a/R/generate_makevars_sources.R
+++ b/inst/generate_makevars_sources.R
@@ -5,10 +5,10 @@ cpp <- list.files(
   full.names = TRUE
 )
 
-# strip leading "src/"
-cpp <- sub("^src/", "", cpp)
+# strip leading "src/" (MacOs/ Linux) or leading "src\\" (Windows)
+cpp <- sub("^src[\\\\/]", "", cpp)
 
-con <- file("src/sources.mk", open = "w")
+con <- file(file.path("src", "sources.mk"), open = "w")
 
 writeLines(c(
   "# ------------------------------------------------------------------",