a fix for running on Mac OS X El Capitan

com.oracle.truffle.r.native/Makefile

@@ -27,6 +27,7 @@
 
 export TOPDIR = $(CURDIR)
 export FASTR_R_HOME=$(abspath $(TOPDIR)/..)
+export FASTR_LIB_DIR=$(FASTR_R_HOME)/lib
 export R_VERSION = 3.1.3
 export GNUR_HOME = $(TOPDIR)/gnur/R-$(R_VERSION)
 

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

@@ -36,7 +36,7 @@ endif
 
 SRC = src
 OBJ = lib
-LIBDIR = $(TOPDIR)/../lib
+LIBDIR = $(abspath $(TOPDIR)/../lib)
 
 C_SOURCES := $(wildcard $(SRC)/*.c)
 
@@ -56,17 +56,19 @@ $(C_OBJECTS): | $(OBJ)
 $(OBJ):
 	mkdir -p $(OBJ)
 
-# On Darwin we need to create a libR.dylib as the libRlapack library has a dependency on libR
-# We also use this as the "entry library" and establish dependencies on all the shared libraries
-# that we need
+# On Darwin we need to create a libR.dylib in which xerbla goes 
+# as the libRlapack library has a dependency on libR and expecte xerbla to
+# be defined there. We could fix this if we cared by not using the GnuR instance of the 
+# libRlapack and rebuilding it from scratch.
+
 ifeq ($(OS_NAME), Darwin)
 LIB_R := $(LIBDIR)/libR$(DYLIB_EXT)
 
 libr: $(LIB_R)
 
-$(LIB_R): $(OBJ)/rlib_dummy.o
+$(LIB_R): $(OBJ)/xerbla.o
 	mkdir -p $(LIBDIR)
-	$(DYLIB_LD) $(DYLIB_LDFLAGS) -o $(LIB_R) -current_version $(R_VERSION) -compatibility_version $(R_VERSION) $(OBJ)/rlib_dummy.o
+	$(DYLIB_LD) $(DYLIB_LDFLAGS) -o $(LIB_R) -current_version $(R_VERSION) -compatibility_version $(R_VERSION) $(OBJ)/xerbla.o
 
 cleanlibr:
 	rm -f $(LIB_R)

com.oracle.truffle.r.native/builtinlibs/src/rlib_dummy.c

-/*
- * Copyright (c) 2015, 2015, Oracle and/or its affiliates. All rights reserved.
- * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
- *
- * This code is free software; you can redistribute it and/or modify it
- * under the terms of the GNU General Public License version 2 only, as
- * published by the Free Software Foundation.
- *
- * This code is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
- * version 2 for more details (a copy is included in the LICENSE file that
- * accompanied this code).
- *
- * You should have received a copy of the GNU General Public License version
- * 2 along with this work; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
- * or visit www.oracle.com if you need additional information or have any
- * questions.
- */
-
-// empty file for now

com.oracle.truffle.r.native/gnur/Makefile.libs

@@ -27,7 +27,7 @@ ifneq ($(MAKECMDGOALS),clean)
 include $(TOPDIR)/platform.mk
 endif
 
-TARGET_DIR := $(TOPDIR)/../lib
+TARGET_DIR := $(abspath $(TOPDIR)/../lib)
 BLAS_TARGET := $(TARGET_DIR)/libRblas$(DYLIB_EXT)
 LAPACK_TARGET := $(TARGET_DIR)/libRlapack$(DYLIB_EXT)
 PCRE_TARGET := $(TARGET_DIR)/libpcre$(DYLIB_EXT)
@@ -42,6 +42,10 @@ $(BLAS_TARGET): $(GNUR_HOME)/lib/libRblas$(DYLIB_EXT)
 
 $(LAPACK_TARGET): $(GNUR_HOME)/lib/libRlapack$(DYLIB_EXT)
 	cp $(GNUR_HOME)/lib/libRlapack$(DYLIB_EXT) $(LAPACK_TARGET)
+ifeq ($(OS_NAME),Darwin)
+	install_name_tool -change libRblas.dylib $(BLAS_TARGET) $(LAPACK_TARGET)
+	install_name_tool -change libR.dylib $(TARGET_DIR)/libR.dylib $(LAPACK_TARGET)
+endif
 
 PCRE_OBJS := $(wildcard $(GNUR_HOME)/src/extra/pcre/pcre_*.o)
 

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

@@ -24,7 +24,7 @@
 .PHONY: all clean libdir make_subdirs clean_subdirs
 
 SUBDIRS = base compiler datasets utils grDevices graphics grid parallel splines stats methods tools fastr
-export FASTR_LIBDIR = $(TOPDIR)/../library
+export FASTR_LIBRARY_DIR = $(abspath $(TOPDIR)/../library)
 
 all: libdir make_subdirs
 
@@ -41,4 +41,4 @@ clean_subdirs:
 	done
 	
 libdir:
-	mkdir -p $(FASTR_LIBDIR)
+	mkdir -p $(FASTR_LIBRARY_DIR)

com.oracle.truffle.r.native/library/base/Makefile

@@ -21,7 +21,7 @@
 # questions.
 #
 
-RPROFILE := $(FASTR_LIBDIR)/base/R/Rprofile
+RPROFILE := $(FASTR_LIBRARY_DIR)/base/R/Rprofile
 RPROFILE_ORIG := $(RPROFILE).orig
 LIB_PKG_POST = $(RPROFILE)
 

com.oracle.truffle.r.native/library/fastr/Makefile

@@ -32,7 +32,7 @@
 .PHONY: all
 
 PKG_FILES = $(shell find src/ -type f -name '*')
-INSTALL_SENTINEL = $(FASTR_LIBDIR)/fastr/DESCRIPTION
+INSTALL_SENTINEL = $(FASTR_LIBRARY_DIR)/fastr/DESCRIPTION
 
 PKG_TAR = lib/fastr.tar
 
@@ -43,7 +43,7 @@ $(PKG_TAR): $(PKG_FILES)
 	(cd src; tar cf ../$(PKG_TAR) *)
 
 $(INSTALL_SENTINEL): $(PKG_TAR)
-	$(GNUR_HOME)/bin/R CMD INSTALL --library=$(FASTR_LIBDIR) src
+	$(GNUR_HOME)/bin/R CMD INSTALL --library=$(FASTR_LIBRARY_DIR) src
 	
 clean:
 	rm -f $(PKG_TAR)

com.oracle.truffle.r.native/library/lib.mk

@@ -25,7 +25,7 @@
 # The common part of the archive (everything except the .so) is created
 # by copying the directory in the GnuR build. Then the FastR .so file is created
 # and overwrites the default. The libraries are stored in the directory denoted
-# FASTR_LIBDIR.
+# FASTR_LIBRARY_DIR.
 
 # A package that requires special processing before the library is built should
 # define LIB_PKG_PRE and for post processing define LIB_PKG_POST in its Makefile.
@@ -66,7 +66,7 @@ FFI_INCLUDES = -I$(TOPDIR)/include -I$(TOPDIR)/include/R_ext
 
 INCLUDES := $(JNI_INCLUDES) $(FFI_INCLUDES)
 
-PKGDIR := $(FASTR_LIBDIR)/$(PKG)
+PKGDIR := $(FASTR_LIBRARY_DIR)/$(PKG)
 
 ifneq ($(C_SOURCES),)
 all: $(LIB_PKG_PRE) libcommon $(LIB_PKG) $(LIB_PKG_POST)
@@ -77,8 +77,8 @@ endif
 libcommon: $(PKGDIR)
 
 $(PKGDIR): $(GNUR_HOME)/library/$(PKG)
-	(cd $(GNUR_HOME)/library; tar cf - $(PKG)) | (cd $(FASTR_LIBDIR); tar xf -)
-	touch $(FASTR_LIBDIR)/$(PKG)
+	(cd $(GNUR_HOME)/library; tar cf - $(PKG)) | (cd $(FASTR_LIBRARY_DIR); tar xf -)
+	touch $(FASTR_LIBRARY_DIR)/$(PKG)
 
 $(C_OBJECTS): | $(OBJ)
 
@@ -90,8 +90,16 @@ $(OBJ):
 $(LIB_PKG): $(C_OBJECTS) $(F_OBJECTS) $(PKGDIR)
 	mkdir -p $(LIBDIR)
 	$(DYLIB_LD) $(DYLIB_LDFLAGS) -o $(LIB_PKG) $(C_OBJECTS) $(F_OBJECTS) $(PKG_LIBS)
-	mkdir -p $(FASTR_LIBDIR)/$(PKG)/libs
-	cp $(LIB_PKG) $(FASTR_LIBDIR)/$(PKG)/libs
+	mkdir -p $(FASTR_LIBRARY_DIR)/$(PKG)/libs
+	cp $(LIB_PKG) $(FASTR_LIBRARY_DIR)/$(PKG)/libs
+# find a way to move into stats makefile (using LIB_PKG_POST)
+ifeq ($(OS_NAME),Darwin)
+ifeq ($(PACKAGE),stats)
+	install_name_tool -change libRblas.dylib $(FASTR_R_HOME)/lib/libRblas.dylib $(FASTR_LIBRARY_DIR)/$(PKG)/libs/$(PKG).so
+	install_name_tool -change libRlapack.dylib $(FASTR_R_HOME)/lib/libRlapack.dylib $(FASTR_LIBRARY_DIR)/$(PKG)/libs/$(PKG).so
+	install_name_tool -change libappl.dylib $(FASTR_R_HOME)/lib/libappl.dylib $(FASTR_LIBRARY_DIR)/$(PKG)/libs/$(PKG).so
+endif
+endif
 
 $(OBJ)/%.o: $(SRC)/%.c $(H_SOURCES)
 	$(CC) $(CFLAGS) $(INCLUDES) -c $< -o $@
@@ -101,5 +109,5 @@ $(OBJ)/%.o: $(SRC)/%.f
 
 clean: $(CLEAN_PKG)
 	rm -rf $(LIBDIR)/*
-	rm -rf $(FASTR_LIBDIR)/$(PKG)
+	rm -rf $(FASTR_LIBRARY_DIR)/$(PKG)
 

com.oracle.truffle.r.native/library/stats/Makefile

@@ -27,12 +27,13 @@ LIB_PKG_PRE = $(OBJ)/fft.o
 GNUR_FFT := $(GNUR_HOME)/src/library/stats/src/fft.c
 CLEAN_PKG := cleanfft
 
-# have to incldue this here for PKG_LIBS
+
+# have to include this here for PKG_LIBS
 ifneq ($(MAKECMDGOALS),clean)
 include $(TOPDIR)/platform.mk
 endif
 
-PKG_LIBS := $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS := $(LAPACK_LIBS) $(BLAS_LIBS) -lappl -L$(FASTR_LIB_DIR) $(FLIBS)
 
 include ../lib.mk
 

com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/LibPaths.java

@@ -29,6 +29,13 @@ import com.oracle.truffle.r.runtime.RPlatform.*;
 
 public class LibPaths {
 
+    /**
+     * Returns the absolute path to the directory containing the builtin libraries.
+     */
+    public static String getBuiltinLibPath() {
+        return FileSystems.getDefault().getPath(REnvVars.rHome(), "lib").toString();
+    }
+
     /**
      * Returns the absolute path to the builtin library {@code libName} for use with
      * {@link System#load}.

com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/jnr/JNR_Lapack.java

@@ -82,7 +82,7 @@ public class JNR_Lapack implements LapackRFFI {
         }
     }
 
-    private static Lapack lapack() {
+    static Lapack lapack() {
         return LapackProvider.lapack();
     }
 

com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/jnr/JNR_RFFIFactory.java

@@ -22,6 +22,7 @@
  */
 package com.oracle.truffle.r.runtime.ffi.jnr;
 
+import com.oracle.truffle.r.runtime.RPlatform;
 import com.oracle.truffle.r.runtime.context.*;
 import com.oracle.truffle.r.runtime.context.RContext.ContextState;
 import com.oracle.truffle.r.runtime.ffi.*;
@@ -44,12 +45,19 @@ public class JNR_RFFIFactory extends RFFIFactory implements RFFI {
          * Some package C code calls these functions and, therefore, expects the linpack symbols to
          * be available, which will not be the case unless one of the functions has already been
          * called from R code. So we eagerly load the library to define the symbols.
+         * 
+         * There is an additional problem when running without a *_LIBRARY_PATH being set which is
+         * mandated by Mac OSX El Capitan, which is we must tell JNR where to find the libraries.
          */
+        String jnrLibPath = LibPaths.getBuiltinLibPath();
+        if (RPlatform.getOSInfo().osName.equals("Mac OS X")) {
+            // Why this is necessary is a JNR mystery
+            jnrLibPath += ":/usr/lib";
+        }
+        System.setProperty("jnr.ffi.library.path", jnrLibPath);
         JNR_RAppl.linpack();
-        /*
-         * Same for Rlapack (used by stats).
-         */
-        getLapackRFFI().ilaver(new int[3]);
+        JNR_Lapack.lapack();
+
     }
 
     /**

mx.fastr/mx_fastr.py

@@ -142,24 +142,21 @@ def _get_ldpaths(lib_env_name):
 def setREnvironment():
     '''
     If R is run via mx, then the library path will not be set, whereas if it is
-    run from 'bin/R' it will be, via etc/ldpaths. Except that in the latter case
-    on Darwin we still need to add /usr/lib to so that JNR can resolve libc for RFFI.
+    run from 'bin/R' it will be, via etc/ldpaths.
+    On Mac OS X El Capitan and beyond, this is moot as the variable is not
+    passed down. It is TBD if we can avoid this on Linux.
     '''
     os.environ['R_HOME'] = _fastr_suite.dir
     osname = platform.system()
-    if osname == 'Darwin':
-        lib_env = 'DYLD_FALLBACK_LIBRARY_PATH'
-    else:
+    if osname != 'Darwin':
         lib_env = 'LD_LIBRARY_PATH'
 
-    if os.environ.has_key(lib_env):
-        lib_value = os.environ[lib_env]
-    else:
-        lib_value = _get_ldpaths(lib_env)
+        if os.environ.has_key(lib_env):
+            lib_value = os.environ[lib_env]
+        else:
+            lib_value = _get_ldpaths(lib_env)
 
-    if osname == 'Darwin':
-        lib_value = lib_value + os.pathsep + '/usr/lib'
-    os.environ[lib_env] = lib_value
+        os.environ[lib_env] = lib_value
 
 def get_default_jdk():
     '''