diff --git a/com.oracle.truffle.r.native/builtinlibs/Makefile b/com.oracle.truffle.r.native/builtinlibs/Makefile
index cb12f95b38c02b4bbdcf1a2161a126837999a6db..723a87ff996a88ab959e4e90d4fde44c2d1cc328 100644
--- a/com.oracle.truffle.r.native/builtinlibs/Makefile
+++ b/com.oracle.truffle.r.native/builtinlibs/Makefile
@@ -28,7 +28,9 @@
 # that refers to GnuR-internal symbols.
 #
 
+ifneq ($(MAKECMDGOALS),clean)
 include $(TOPDIR)/platform.mk
+endif
 
 .PHONY: all clean cleanlib cleanobj force libr
 
diff --git a/com.oracle.truffle.r.native/fficall/jni/Makefile b/com.oracle.truffle.r.native/fficall/jni/Makefile
index 273f98512c54180795a018befdeb8cc0ce1e629d..3f14954c3d05028a97f150177b016fb825426240 100644
--- a/com.oracle.truffle.r.native/fficall/jni/Makefile
+++ b/com.oracle.truffle.r.native/fficall/jni/Makefile
@@ -25,7 +25,9 @@ ifeq ($(TOPDIR),)
     TOPDIR = $(abspath ../..)
 endif
 
+ifneq ($(MAKECMDGOALS),clean)
 include $(TOPDIR)/platform.mk
+endif
 
 .PHONY: all clean
 
diff --git a/com.oracle.truffle.r.native/gnur/Makefile.gnur b/com.oracle.truffle.r.native/gnur/Makefile.gnur
index c5c581f7edf8e4437233f6d190d50ef10939a795..108538b086c6ca8e1a27d811fef703e16a1de343 100644
--- a/com.oracle.truffle.r.native/gnur/Makefile.gnur
+++ b/com.oracle.truffle.r.native/gnur/Makefile.gnur
@@ -77,6 +77,11 @@ build: $(GNUR_DIR)/bin/R
 $(GNUR_DIR)/bin/R: $(GNUR_DIR)/Makeconf 
 	(cd $(GNUR_DIR); make >& gnur_make.log)
 
+HAVE_MAKEFILE := $(shell [ -f $(GNUR_DIR)/Makefile ] && echo "Makefile.exists")
+ifeq ($(HAVE_MAKEFILE),Makefile.exists)
 clean:
 	rm -f Makeconf.done
 	(cd $(GNUR_DIR); make distclean)
+else
+clean:
+endif
diff --git a/com.oracle.truffle.r.native/gnur/Makefile.libs b/com.oracle.truffle.r.native/gnur/Makefile.libs
index ca45fa3b5ac046e2ea5e6c6074bc72f62f645600..43739766d25a33931b64a66ecc3cf120b5b94f43 100644
--- a/com.oracle.truffle.r.native/gnur/Makefile.libs
+++ b/com.oracle.truffle.r.native/gnur/Makefile.libs
@@ -23,7 +23,9 @@
 
 # Copies the Blas and lapack libraries and builds the pcre library
 
+ifneq ($(MAKECMDGOALS),clean)
 include $(TOPDIR)/platform.mk
+endif
 
 TARGET_DIR := $(TOPDIR)/builtinlibs/lib
 BLAS_TARGET := $(TARGET_DIR)/libRblas$(DYLIB_EXT)
diff --git a/com.oracle.truffle.r.native/library/lib.mk b/com.oracle.truffle.r.native/library/lib.mk
index 4e129f6588410f8e9a9408c8d75b6d11c0927112..c9322d1ca0ae2f2ae5bc9f6dafe05c5399e7a0f7 100644
--- a/com.oracle.truffle.r.native/library/lib.mk
+++ b/com.oracle.truffle.r.native/library/lib.mk
@@ -30,7 +30,9 @@
 # A package that requires special processing before the library is built should
 # define LIB_PKG_PRE and for post processing define LIB_PKG_POST
 
+ifneq ($(MAKECMDGOALS),clean)
 include $(TOPDIR)/platform.mk
+endif
 
 .PHONY: all clean cleanlib cleanobj force libr libcommon 
 
diff --git a/com.oracle.truffle.r.test.native/packages/testrffi/src/src/Makefile b/com.oracle.truffle.r.test.native/packages/testrffi/src/src/Makefile
index ca69da5ac04840c5c2c7f814fb20b0d48b5905f3..4419b3fcf6ca589a9fce7750a9e473ddb0d5cfe8 100644
--- a/com.oracle.truffle.r.test.native/packages/testrffi/src/src/Makefile
+++ b/com.oracle.truffle.r.test.native/packages/testrffi/src/src/Makefile
@@ -29,7 +29,9 @@ C_OBJECTS := $(C_SOURCES:.c=.o)
 C_LIB := testrffi.so
 
 NATIVE_PROJECT=$(FASTR_HOME)/com.oracle.truffle.r.native
+ifneq ($(MAKECMDGOALS),clean)
 include $(NATIVE_PROJECT)/platform.mk
+endif
 
 ifeq ($(FASTR_INSTALL), GNUR)
     INCLUDES := -I $(R_HOME)/include
diff --git a/com.oracle.truffle.r.test.native/urand/Makefile b/com.oracle.truffle.r.test.native/urand/Makefile
index 65bb933d03492b3a15894ce6d684d6a19fa1c441..4fe68d6161ab4deca02ae284c9f326733b4ee0cc 100644
--- a/com.oracle.truffle.r.test.native/urand/Makefile
+++ b/com.oracle.truffle.r.test.native/urand/Makefile
@@ -27,7 +27,9 @@ endif
 
 NATIVE_PROJECT = $(subst test.native,native,$(TOPDIR))
 
+ifneq ($(MAKECMDGOALS),clean)
 include $(NATIVE_PROJECT)/platform.mk
+endif
 
 .PHONY: all clean
 
diff --git a/com.oracle.truffle.r.test/rpackages/rffi/testrffi/src/Makefile b/com.oracle.truffle.r.test/rpackages/rffi/testrffi/src/Makefile
index 73ab7c69aa06a6946d2b577df850a4b6a1b7cb3f..abd870b1148f9c7826a34e9d4da7bb2df52f9273 100644
--- a/com.oracle.truffle.r.test/rpackages/rffi/testrffi/src/Makefile
+++ b/com.oracle.truffle.r.test/rpackages/rffi/testrffi/src/Makefile
@@ -29,7 +29,9 @@ C_OBJECTS := $(C_SOURCES:.c=.o)
 C_LIB := testrffi.so
 
 NATIVE_PROJECT=$(FASTR_HOME)/com.oracle.truffle.r.native
+ifneq ($(MAKECMDGOALS),clean)
 include $(NATIVE_PROJECT)/platform.mk
+endif
 
 ifeq ($(FASTR_INSTALL), GNUR)
     INCLUDES := -I $(R_HOME)/include