[GR-7687] [GR-7329] Incorrect use of Rscript in package testing.

PullRequest: fastr/1319

com.oracle.truffle.r.test.packages.analyzer/src/com/oracle/truffle/r/test/packages/analyzer/parser/LogFileParser.java

@@ -103,11 +103,18 @@ public class LogFileParser {
                 this.reader = r;
                 consumeLine();
 
+                // consume any leading lines (there might be some output of 'mx')
+                collectBody(Token.BEGIN_INSTALL_TEST);
+
                 Section installTest0 = parseInstallTest();
                 logFile.addSection(installTest0);
                 if (!installTest0.isSuccess()) {
                     return logFile;
                 }
+
+                // again, consume any leading lines
+                collectBody(Token.BEGIN_INSTALL_TEST);
+
                 Section installTest1 = parseInstallTest();
                 logFile.addSection(installTest1);
                 if (installTest1.isSuccess()) {

com.oracle.truffle.r.test.packages/r/install.cache.R

@@ -21,6 +21,10 @@
 # questions.
 #
 
+is.fastr <- function() {
+    length(grep('FastR', R.Version()$version.string))
+}
+
 # A simple log function; to be replaced by a user of this file.
 log.message <- function(..., level=0) {
     cat(..., "\n")
@@ -255,7 +259,7 @@ recommended.base.packages <- c("boot", "class", "cluster", "codetools", "foreign
 base.packages <- c("base", "compiler", "datasets", "grDevices", "graphics", "grid", "methods", "parallel", "splines", "stats", "stats4", "tools", "utils")
 
 # the list of packages that will be excluded in the transitive dependecies
-ignored.packages <- recommended.base.packages
+ignored.packages <- if (is.fastr()) recommended.base.packages else base.packages
 
 package.dependencies <- function(pkg, lib, dependencies = c("Depends", "Imports", "LinkingTo"), pl = available.packages()) {
     if (!(pkg %in% rownames(pl))) {

com.oracle.truffle.r.test.packages/r/install.packages.R

@@ -135,6 +135,8 @@ trim <- function (x) gsub("^\\s+|\\s+$", "", x)
 
 strip.version <- function(x) gsub("\\s*\\(.*\\)$", "", x)
 
+initial.packages <- c("methods", "datasets", "utils", "grDevices", "graphics", "stats")
+
 default.packages <- c("R", "base", "grid", "splines", "utils",
 		"compiler", "grDevices", "methods", "stats", "stats4",
 		"datasets", "graphics", "parallel", "tools", "tcltk")
@@ -857,12 +859,16 @@ is.fastr <- function() {
 
 system.test <- function(pkgname) {
 	script <- normalizePath("com.oracle.truffle.r.test.packages/r/test.package.R")
+    options <- character(0)
 	if (is.fastr()) {
 		rscript = file.path(R.home(), "bin", "Rscript")
 	} else {
-		rscript = gnu_rscript()
+        # GnuR's Rscript command does not load the 'methods' package by default.
+        # But the examples are assumed to be run in a shell where the package is on the search path.
+	    options <- paste0("--default-packages=", paste0(initial.packages, collapse=","))
+        rscript = gnu_rscript()
 	}
-	args <- c(script, pkgname, file.path(testdir, pkgname), lib.install)
+	args <- c(options, script, pkgname, file.path(testdir, pkgname), lib.install)
 	# we want to stop tests that hang, but some packages have many tests
 	# each of which spawns a sub-process (over which we have no control)
 	# so we time out the entire set after 20 minutes.