From ec181bebfe7d1ad765e389ddb6a42643d7924914 Mon Sep 17 00:00:00 2001
From: Zbynek Slajchrt <zbynek.slajchrt@oracle.com>
Date: Wed, 21 Mar 2018 14:58:58 +0100
Subject: [PATCH] FastR installs MRAN packages by default
---
.../oracle/truffle/r/library/utils/R/utils.R | 50 +++++++++++++++++++
com.oracle.truffle.r.native/Makefile | 1 +
com.oracle.truffle.r.native/run/Makefile | 5 +-
.../oracle/truffle/r/runtime/REnvVars.java | 19 +++++++
.../oracle/truffle/r/runtime/ROptions.java | 5 ++
.../r/install.packages.R | 8 ++-
6 files changed, 86 insertions(+), 2 deletions(-)
create mode 100644 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/utils/R/utils.R
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/utils/R/utils.R b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/utils/R/utils.R
new file mode 100644
index 0000000000..d911e336fa
--- /dev/null
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/utils/R/utils.R
@@ -0,0 +1,50 @@
+# Copyright (c) 2018, 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.
+
+eval(expression({
+ excludedPkgs <- c("rJava")
+ excludedPkgsMsgs <- c("CRAN rJava is not supported on FastR, but you can download and install rJava compatible replacement package from https://github.com/oracle/fastr/master/com.oracle.truffle.r.pkgs/rJava")
+
+ fastRPkgFilter <- function (av) {
+ # The following statement will assign the url of the FastR clone of rJava, when ready (possibly on GitHub).
+ #av["rJava","Repository"] <- "https://github.com/oracle/fastr/master/com.oracle.truffle.r.pkgs/rJava"
+ found <- rownames(av) %in% excludedPkgs
+ if (any(found)) {
+ av <- av[-which(found),]
+ }
+ av
+ }
+ options(available_packages_filters = list(add = TRUE, fastRPkgFilter))
+
+ getDependencies.original <- getDependencies
+ getDependencies <- function(pkgs, dependencies = NA, available = NULL, lib = .libPaths()[1L], binary = FALSE) {
+ res <- getDependencies.original(pkgs, dependencies, available, lib, binary)
+
+ found <- excludedPkgs %in% pkgs
+ if (any(found)) {
+ foundPkgMsgs <- excludedPkgsMsgs[which(found)]
+ warning(paste(foundPkgMsgs, collapse="\n"), call. = FALSE)
+ }
+
+ res
+ }
+
+}), asNamespace("utils"))
\ No newline at end of file
diff --git a/com.oracle.truffle.r.native/Makefile b/com.oracle.truffle.r.native/Makefile
index 159c2720d3..3f7f4f4f7f 100644
--- a/com.oracle.truffle.r.native/Makefile
+++ b/com.oracle.truffle.r.native/Makefile
@@ -28,6 +28,7 @@ export FASTR_R_HOME=$(abspath $(TOPDIR)/..)
export FASTR_LIB_DIR=$(FASTR_R_HOME)/lib
export FASTR_NATIVE_DIR = $(TOPDIR)
export R_VERSION = 3.4.0
+export DEFAULT_CRAN_MIRROR = "https://mran.microsoft.com/snapshot/2018-03-20"
export GNUR_HOME = $(TOPDIR)/gnur/patch-build
ifeq ($(FASTR_RFFI),llvm)
diff --git a/com.oracle.truffle.r.native/run/Makefile b/com.oracle.truffle.r.native/run/Makefile
index 4f6aa77dec..13f2a596fb 100644
--- a/com.oracle.truffle.r.native/run/Makefile
+++ b/com.oracle.truffle.r.native/run/Makefile
@@ -1,5 +1,5 @@
#
-# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2018, 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
@@ -87,6 +87,9 @@ $(FASTR_BIN_DIR)/R: Makefile R.sh Rscript.sh Rscript_exec.sh Rclasspath.sh
cp $(GNUR_HOME_BINARY)/etc/repositories $(FASTR_ETC_DIR)/repositories
cp $(GNUR_HOME_BINARY)/etc/ldpaths $(FASTR_ETC_DIR)/ldpaths
ed Makeconf.etc < edMakeconf.etc
+
+ echo $(DEFAULT_CRAN_MIRROR) > $(FASTR_ETC_DIR)/DEFAULT_CRAN_MIRROR
+
ifeq ($(FASTR_RFFI),llvm)
ed Makeconf.etc < edMakeconf.etc.llvm
cp $(LLVM_TOOLS) $(FASTR_BIN_DIR)
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/REnvVars.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/REnvVars.java
index c9103b3d8c..918258922b 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/REnvVars.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/REnvVars.java
@@ -303,6 +303,25 @@ public final class REnvVars implements RContext.ContextState {
return TimeZone.getDefault();
}
+ public static String getCRANMirror() {
+ String cranMirror = System.getenv("CRAN_MIRROR");
+ if (cranMirror == null) {
+ Path defCranMirrorPath = Paths.get(REnvVars.rHome()).resolve("etc").resolve("DEFAULT_CRAN_MIRROR");
+ if (!Files.exists(defCranMirrorPath)) {
+ throw RSuicide.rSuicide("Missing etc/DEFAULT_CRAN_MIRROR file");
+ }
+ List<String> cranMirrors;
+ try {
+ cranMirrors = Files.readAllLines(defCranMirrorPath);
+ } catch (IOException e) {
+ throw RSuicide.rSuicide("Invalid etc/DEFAULT_CRAN_MIRROR file");
+ }
+ assert !cranMirrors.isEmpty();
+ cranMirror = cranMirrors.get(0);
+ }
+ return cranMirror;
+ }
+
private String expandParameters(String value) {
StringBuilder result = new StringBuilder();
int x = 0;
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/ROptions.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/ROptions.java
index ba250c7d6b..7bce52aded 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/ROptions.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/ROptions.java
@@ -175,6 +175,11 @@ public class ROptions {
map.put("browserNLdisabled", RDataFactory.createSharedLogicalVectorFromScalar(false));
boolean cBoundsCheck = optionFromEnvVar("R_C_BOUNDS_CHECK", envVars);
map.put("CBoundsCheck", RDataFactory.createSharedLogicalVectorFromScalar(cBoundsCheck));
+
+ String cranMirror = REnvVars.getCRANMirror();
+ if (cranMirror != null) {
+ map.put("repos", cranMirror);
+ }
}
private static boolean optionFromEnvVar(String envVar, REnvVars envVars) {
diff --git a/com.oracle.truffle.r.test.packages/r/install.packages.R b/com.oracle.truffle.r.test.packages/r/install.packages.R
index acb13821f8..7dac0bf7bd 100644
--- a/com.oracle.truffle.r.test.packages/r/install.packages.R
+++ b/com.oracle.truffle.r.test.packages/r/install.packages.R
@@ -1,5 +1,5 @@
#
-# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2018, 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
@@ -304,6 +304,12 @@ set.repos <- function() {
} else if (name == "FASTR") {
# set the FastR internal repo
repos[["FASTR"]] <- paste0("file://", normalizePath("com.oracle.truffle.r.test.native/packages/repo"))
+ } else if (name == "SNAPSHOT") {
+ con <- file("etc/DEFAULT_CRAN_MIRROR", "r");
+ tryCatch({
+ cran.mirror <<- readLines(con)[[1]]
+ }, finally=function() close(con))
+ repos[["CRAN"]] <- cran.mirror
} else {
# User defined
repos[[name]] <- uri
--
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