Fix linker issues when running C++ built by the LLVM toolchain in native mode

(cherry picked from commit 95fa369)

Author: steve-s

com.oracle.truffle.r.native/run/Makefile

@@ -89,7 +89,11 @@ $(FASTR_BIN_DIR)/R: Makefile R.sh Rscript.sh Rscript_exec.sh Rclasspath.sh
 	cp $(GNUR_HOME_BINARY)/etc/Makeconf Makeconf.etc
 	cp $(GNUR_HOME_BINARY)/etc/javaconf $(FASTR_ETC_DIR)/javaconf
 	cp $(GNUR_HOME_BINARY)/etc/repositories $(FASTR_ETC_DIR)/repositories
-	cp $(GNUR_HOME_BINARY)/etc/ldpaths $(FASTR_ETC_DIR)/ldpaths
+	# ldpaths: create two versions: ldpaths.llvm (used also as default ldpaths) and ldpaths.native
+	# the llvm version adds the LLVM lib folder to the LD_LIBRARY_PATH
+	sed 's!export LD_LIBRARY_PATH!LD_LIBRARY_PATH="$$\{R_HOME\}/../llvm/native/lib/:$$\{LD_LIBRARY_PATH\}"; export LD_LIBRARY_PATH!' $(GNUR_HOME_BINARY)/etc/ldpaths > $(FASTR_ETC_DIR)/ldpaths
+	cp $(FASTR_ETC_DIR)/ldpaths $(FASTR_ETC_DIR)/ldpaths.llvm
+	cp $(GNUR_HOME_BINARY)/etc/ldpaths $(FASTR_ETC_DIR)/ldpaths.native
 	# the ed script adds -DFASTR to compiler options and removes JAVA related variables
 	ed Makeconf.etc < edMakeconf.etc
 	# Backup the current state of Makeconf.etc to allow users to switch back to the native toolchain

com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/fastr/FastRSetToolchain.java

@@ -52,19 +52,25 @@ public abstract class FastRSetToolchain extends RBuiltinNode.Arg1 {
     @Specialization
     protected RNull setToolchain(String name) {
         String srcConf;
+        String srcLdpaths;
         if ("native".equals(name)) {
             srcConf = "Makeconf.native";
+            srcLdpaths = "ldpaths.native";
         } else if ("llvm".equals(name)) {
             srcConf = "Makeconf.llvm";
+            srcLdpaths = "ldpaths.llvm";
         } else {
             throw error(RError.Message.GENERIC, "Only 'native' or 'llvm' argument values accepted");
         }
         TruffleFile rHome = REnvVars.getRHomeTruffleFile(RContext.getInstance().getEnv());
         TruffleFile etc = rHome.resolve("etc");
-        TruffleFile src = etc.resolve(srcConf);
-        TruffleFile dst = etc.resolve("Makeconf");
+        TruffleFile srcConfFile = etc.resolve(srcConf);
+        TruffleFile dstConfFile = etc.resolve("Makeconf");
+        TruffleFile srcLdpathsFile = etc.resolve(srcLdpaths);
+        TruffleFile dstLdpathsFile = etc.resolve("ldpaths");
         try {
-            src.copy(dst, StandardCopyOption.REPLACE_EXISTING);
+            srcConfFile.copy(dstConfFile, StandardCopyOption.REPLACE_EXISTING);
+            srcLdpathsFile.copy(dstLdpathsFile, StandardCopyOption.REPLACE_EXISTING);
         } catch (IOException e) {
             throw new RInternalError(String.format("Copying %s over etc/Makeconf failed", srcConf), e);
         }