From 205a8b222e7bff2207524db5edc7c1d45a38b9c4 Mon Sep 17 00:00:00 2001
From: Mick Jordan <mick.jordan@oracle.com>
Date: Fri, 4 Dec 2015 15:51:40 -0800
Subject: [PATCH] a fix for running on Mac OS X El Capitan
---
com.oracle.truffle.r.native/Makefile | 1 +
.../builtinlibs/Makefile | 14 ++++++-----
.../builtinlibs/src/rlib_dummy.c | 24 -------------------
.../gnur/Makefile.libs | 6 ++++-
com.oracle.truffle.r.native/library/Makefile | 4 ++--
.../library/base/Makefile | 2 +-
.../library/fastr/Makefile | 4 ++--
com.oracle.truffle.r.native/library/lib.mk | 22 +++++++++++------
.../library/stats/Makefile | 5 ++--
.../truffle/r/runtime/ffi/LibPaths.java | 7 ++++++
.../truffle/r/runtime/ffi/jnr/JNR_Lapack.java | 2 +-
.../r/runtime/ffi/jnr/JNR_RFFIFactory.java | 16 +++++++++----
mx.fastr/mx_fastr.py | 21 +++++++---------
13 files changed, 66 insertions(+), 62 deletions(-)
delete mode 100644 com.oracle.truffle.r.native/builtinlibs/src/rlib_dummy.c
diff --git a/com.oracle.truffle.r.native/Makefile b/com.oracle.truffle.r.native/Makefile
index b180b74236..98b258d4ae 100644
--- a/com.oracle.truffle.r.native/Makefile
+++ b/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)
diff --git a/com.oracle.truffle.r.native/builtinlibs/Makefile b/com.oracle.truffle.r.native/builtinlibs/Makefile
index b1b3c2a1fb..b6cb85fd5a 100644
--- a/com.oracle.truffle.r.native/builtinlibs/Makefile
+++ b/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 $(LIB_R)
diff --git a/com.oracle.truffle.r.native/builtinlibs/src/rlib_dummy.c b/com.oracle.truffle.r.native/builtinlibs/src/rlib_dummy.c
deleted file mode 100644
index bf7f62896a..0000000000
--- a/com.oracle.truffle.r.native/builtinlibs/src/rlib_dummy.c
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright (c) 2015, 2015, Oracle and/or its affiliates. All rights reserved.
- * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
- *
- * This code is free software; you can redistribute it and/or modify it
- * under the terms of the GNU General Public License version 2 only, as
- * published by the Free Software Foundation.
- *
- * This code is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
- * version 2 for more details (a copy is included in the LICENSE file that
- * accompanied this code).
- *
- * You should have received a copy of the GNU General Public License version
- * 2 along with this work; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
- * or visit www.oracle.com if you need additional information or have any
- * questions.
- */
-
-// empty file for now
diff --git a/com.oracle.truffle.r.native/gnur/Makefile.libs b/com.oracle.truffle.r.native/gnur/Makefile.libs
index c13f94f972..b402a9cdfd 100644
--- a/com.oracle.truffle.r.native/gnur/Makefile.libs
+++ b/com.oracle.truffle.r.native/gnur/Makefile.libs
@@ -27,7 +27,7 @@ ifneq ($(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)
diff --git a/com.oracle.truffle.r.native/library/Makefile b/com.oracle.truffle.r.native/library/Makefile
index fd056e3f36..095d3a0226 100644
--- a/com.oracle.truffle.r.native/library/Makefile
+++ b/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)
diff --git a/com.oracle.truffle.r.native/library/base/Makefile b/com.oracle.truffle.r.native/library/base/Makefile
index 40d2328561..bc26992f4c 100644
--- a/com.oracle.truffle.r.native/library/base/Makefile
+++ b/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)
diff --git a/com.oracle.truffle.r.native/library/fastr/Makefile b/com.oracle.truffle.r.native/library/fastr/Makefile
index 3ceba8fe3c..65312e9288 100644
--- a/com.oracle.truffle.r.native/library/fastr/Makefile
+++ b/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 $(PKG_TAR)
diff --git a/com.oracle.truffle.r.native/library/lib.mk b/com.oracle.truffle.r.native/library/lib.mk
index e525e23d1b..6812f369bd 100644
--- a/com.oracle.truffle.r.native/library/lib.mk
+++ b/com.oracle.truffle.r.native/library/lib.mk
@@ -25,7 +25,7 @@
# The common part of the archive (everything except the .so) is created
# by copying the directory in the GnuR build. Then the FastR .so file is created
# and overwrites the default. The libraries are stored in the directory denoted
-# FASTR_LIBDIR.
+# FASTR_LIBRARY_DIR.
# A package that requires special processing before the library is built should
# define LIB_PKG_PRE and for post processing define LIB_PKG_POST in its Makefile.
@@ -66,7 +66,7 @@ FFI_INCLUDES = -I$(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)
diff --git a/com.oracle.truffle.r.native/library/stats/Makefile b/com.oracle.truffle.r.native/library/stats/Makefile
index a899a33821..3b7c919081 100644
--- a/com.oracle.truffle.r.native/library/stats/Makefile
+++ b/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
diff --git a/com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/LibPaths.java b/com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/LibPaths.java
index 837c51379d..7a4cf8d4ab 100644
--- a/com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/LibPaths.java
+++ b/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}.
diff --git a/com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/jnr/JNR_Lapack.java b/com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/jnr/JNR_Lapack.java
index fedfd56ad6..57d90fdb89 100644
--- a/com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/jnr/JNR_Lapack.java
+++ b/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();
}
diff --git a/com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/jnr/JNR_RFFIFactory.java b/com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/jnr/JNR_RFFIFactory.java
index 3f03f3bba5..2632720fd3 100644
--- a/com.oracle.truffle.r.runtime.ffi/src/com/oracle/truffle/r/runtime/ffi/jnr/JNR_RFFIFactory.java
+++ b/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();
+
}
/**
diff --git a/mx.fastr/mx_fastr.py b/mx.fastr/mx_fastr.py
index e5260fedd0..f28d431e1c 100644
--- a/mx.fastr/mx_fastr.py
+++ b/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():
'''
--
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