[GR-36122] Backport: Update cluster version.

PullRequest: fastr/2686
oracle · Jan 7, 2022 · 78888bd · 78888bd
2 parents 9742cb7 + db086c5
commit 78888bd
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Showing 4 changed files with 77 additions and 20 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,8 @@
 # 22.0.0
 * Adopted [NodeLibrary](https://www.graalvm.org/truffle/javadoc/com/oracle/truffle/api/interop/NodeLibrary.html).
+* In unit tests, use single shared context rather than multiple inner contexts.
+* Update recommended packages:
+  * cluster to version 2.1.2 (2021-04-17)
 
 # 21.3.0
 * Upgrade of [PCRE](https://www.pcre.org/) to PCRE2 version 10.37.

diff --git a/ci.jsonnet b/ci.jsonnet
@@ -1 +1 @@
-{ overlay : '2bdde206f738bed75f31cab12137df1d682d1d6f' }
+{ overlay : '72fd5ca67a4817f8825e0e74741a134d2d963bb5' }
diff --git a/com.oracle.truffle.r.native.recommended/Makefile b/com.oracle.truffle.r.native.recommended/Makefile
@@ -37,7 +37,7 @@ endif
 
 FASTR_R_HOME = $(abspath $(TOPDIR)/..)
 R_VERSION = 4.0.3
-# The package tar balls are copied from $(GNUR_HOME_BINARY_UNPACKED)/src/library/Recommended
+# Most of the package tar balls are copied from $(GNUR_HOME_BINARY_UNPACKED)/src/library/Recommended
 export GNUR_HOME_BINARY_UNPACKED = $(FASTR_R_HOME)/libdownloads/R-$(R_VERSION)
 
 ifndef GNUR_HOME_BINARY
@@ -68,11 +68,27 @@ GNUR_RECOMMENDED_PKGNAMES := codetools
 endif # FASTR_RELEASE
 GNUR_RECOMMENDED_PKGNAMES_TS = $(GNUR_RECOMMENDED_PKGNAMES:=.ts)
 
+# Recommended packages that are used by fastr in a specific version, i.e., taken from other sources than GNUR_RECOMMENDED_BINARY
+PKGS_WITH_CUSTOM_VERSION := cluster rpart
+RPART_TAR := $(FASTR_R_HOME)/libdownloads/rpart.tar.gz
+CLUSTER_TAR := $(FASTR_R_HOME)/libdownloads/cluster.tar.gz
+
 GNUR_RECOMMENDED_TAR_DIR = $(GNUR_HOME_BINARY_UNPACKED)/src/library/Recommended/
-GNUR_RECOMMENDED_TARS := $(foreach pkg, $(GNUR_RECOMMENDED_PKGNAMES),$(GNUR_RECOMMENDED_TAR_DIR)/$(pkg)*.tar.gz)
+# We do not copy all the recommended packages from gnur's directory. Instead, there are some
+# packages that we take from different sources.
+GNUR_RECOMMENDED_TARS := \
+$(foreach pkg, \
+	$(filter-out $(PKGS_WITH_CUSTOM_VERSION),$(GNUR_RECOMMENDED_PKGNAMES)), \
+	$(GNUR_RECOMMENDED_TAR_DIR)/$(pkg)*.tar.gz \
+)
+ALL_RECOMMENDED_TARS := $(GNUR_RECOMMENDED_TARS) $(RPART_TAR) $(CLUSTER_TAR)
+
 ## need to allow parallel installs
 INSTALL_OPTS = --pkglock --data-compress=xz --no-staged-install
 
+$(info GNUR_RECOMMENDED_PKGNAMES = $(GNUR_RECOMMENDED_PKGNAMES))
+$(info ALL_RECOMMENDED_TARS = $(ALL_RECOMMENDED_TARS))
+
 # in managed mode, we do nothing
 ifneq ($(FASTR_RFFI),managed)
 
@@ -84,7 +100,7 @@ ifdef FASTR_RECOMMENDED_BINARY
 
 $(info Using FastR recommended packages binary: $(FASTR_RECOMMENDED_BINARY))
 
-install.recommended: $(GNUR_RECOMMENDED_TARS)
+install.recommended: $(ALL_RECOMMENDED_TARS)
 #	@if ! (mx -p $(FASTR_R_HOME) r-pkgcache --print-api-checksum --vm fastr | tail -n 1 | diff -q $(FASTR_RECOMMENDED_BINARY)/api-checksum.txt -); then \
 #		echo "******************************"; \
 #		echo "ERROR:"; \
@@ -105,7 +121,23 @@ install.recommended: $(GNUR_RECOMMENDED_TARS)
 # If FASTR_RECOMMENDED_BINARY is not defined, we just build the packages
 else 
 
-$(info GNUR_RECOMMENDED_TARS=$(GNUR_RECOMMENDED_TARS))
+RPART_DIR_NAME := bethatkinson-rpart-4020bb4
+RPART_BUILT_TARBALL := rpart_4.1-16.tar.gz
+# rpart package is downloaded as a tarball directly from GitHub. Unfortunately, we have to make some
+# modifications to that tarball - remove `build` directory.
+rpart.ts: $(RPART_TAR)
+	@echo 'Installing recommended package rpart'
+	tar xf $<
+	rm -rf $(RPART_DIR_NAME)/build
+	# This command creates $RPART_BUILT_TARBALL via GNU-R for better compatibility
+	$(GNUR_HOME_BINARY)/bin/R CMD build --no-build-vignettes $(RPART_DIR_NAME)
+	_R_CHECK_INSTALL_DEPENDS_=no FASTR_USE_F2C=true $(FASTR_R_HOME)/bin/R --polyglot CMD INSTALL $(INSTALL_OPTS) --library=$(FASTR_R_HOME)/library $(RPART_BUILT_TARBALL) &> $@.out || (cat $@.out && exit 1)
+	@echo Finished installing recommended package `basename $<`
+
+cluster.ts: $(CLUSTER_TAR)
+	@echo Installing recommended package `basename $<`
+	@_R_CHECK_INSTALL_DEPENDS_=no FASTR_USE_F2C=true $(FASTR_R_HOME)/bin/R --polyglot CMD INSTALL $(INSTALL_OPTS) --library=$(FASTR_R_HOME)/library $< &> $@.out || (cat $@.out && exit 1)
+	@echo Finished installing recommended package `basename $<`
 
 %.ts: $(GNUR_RECOMMENDED_TAR_DIR)%.tgz
 	@echo Installing recommended package `basename $<`

diff --git a/mx.fastr/suite.py b/mx.fastr/suite.py
@@ -1,5 +1,5 @@
 suite = {
-  "mxversion" : "5.282.0",
+  "mxversion" : "5.316.14",
   "name" : "fastr",
   "versionConflictResolution" : "latest",
   "imports" : {
@@ -31,8 +31,8 @@
 
   "repositories" : {
     "snapshots" : {
-        "url" : "https://curio.ssw.jku.at/nexus/content/repositories/snapshots",
-        "licenses" : ["GPLv3"]
+      "url" : "https://curio.ssw.jku.at/nexus/content/repositories/snapshots",
+      "licenses" : ["GPLv3"]
     }
   },
 
@@ -48,24 +48,44 @@
   # libraries that we depend on
   "libraries" : {
     "GNUR" : {
-        "path" : "libdownloads/R-4.0.3.tar.gz", # keep in sync with the GraalVM support distribution
-        "urls" : ["https://cran.rstudio.com/src/base/R-4/R-4.0.3.tar.gz"],
-        "sha1" : "5daba2d63e07a9f39d9b69b68f0642d71213ec5c",
-        "resource" : "true"
+      "path" : "libdownloads/R-4.0.3.tar.gz", # keep in sync with the GraalVM support distribution
+      "urls" : ["https://cran.rstudio.com/src/base/R-4/R-4.0.3.tar.gz"],
+      "sha1" : "5daba2d63e07a9f39d9b69b68f0642d71213ec5c",
+      "resource" : "true"
     },
 
     "F2C" : {
-        "path" : "libdownloads/f2c/src.tgz",
-        "urls" : ["https://lafo.ssw.uni-linz.ac.at/pub/graal-external-deps/f2c/20191129/src.tgz"],
-        "sha1" : "8a26107bf9f82a2dcfa597f15549a412be75e0ee",
-        "resource" : "true"
+      "path" : "libdownloads/f2c/src.tgz",
+      "urls" : ["https://lafo.ssw.uni-linz.ac.at/pub/graal-external-deps/f2c/20191129/src.tgz"],
+      "sha1" : "8a26107bf9f82a2dcfa597f15549a412be75e0ee",
+      "resource" : "true"
     },
 
     "LIBF2C" : {
-        "path" : "libdownloads/f2c/libf2c.zip",
-        "urls" : ["https://lafo.ssw.uni-linz.ac.at/pub/graal-external-deps/f2c/20191129/libf2c.zip"],
-        "sha1" : "e39a00f425f8fc41dde434686080a94e94884f30",
-        "resource" : "true"
+      "path" : "libdownloads/f2c/libf2c.zip",
+      "urls" : ["https://lafo.ssw.uni-linz.ac.at/pub/graal-external-deps/f2c/20191129/libf2c.zip"],
+      "sha1" : "e39a00f425f8fc41dde434686080a94e94884f30",
+      "resource" : "true"
+    },
+
+    # A recommended package "rpart" with a fixed version rather than taken from GNU-R.
+    "RPART" : {
+      "path" : "libdownloads/rpart.tar.gz",
+      "ext" : ".tar.gz",
+      "version" : "4020bb4ee8fd6739bd97e8c39931fa7e3901300c",
+      "urls" : ["https://api.github.com/repos/bethatkinson/rpart/tarball/{version}"],
+      "sha1" : "ec76dbd51acad10bed843a0005ba5fdcf5c7a35d",
+      "resource" : "true"
+    },
+
+    # A recommended package "cluster" with a fixed version rather than taken from GNU-R.
+    "CLUSTER" : {
+      "path" : "libdownloads/cluster.tar.gz",
+      "ext" : ".tar.gz",
+      "version" : "2.1.2",
+      "urls" : ["https://cran.r-project.org/src/contrib/cluster_{version}.tar.gz"],
+      "sha1" : "47763fa44d11e0f2c2feafade3e331c05eda30d1",
+      "resource" : "true"
     },
 
     "XZ-1.8" : {
@@ -342,6 +362,8 @@
 
     "com.oracle.truffle.r.native.recommended" : {
       "dependencies" : [
+        "RPART",
+        "CLUSTER",
         "com.oracle.truffle.r.native",
         "com.oracle.truffle.r.engine",
         "com.oracle.truffle.r.ffi.impl",