From 9471960479210b9413cd6da677dbe14da39cdf39 Mon Sep 17 00:00:00 2001
From: Mick Jordan <mick.jordan@oracle.com>
Date: Wed, 9 Nov 2016 14:43:47 -0800
Subject: [PATCH] pkgtest: refactor to use internal GNU R when possible; misc
other changes for daily recommended packages test
---
.gitignore | 4 +-
.../system/ProcessSystemFunctionFactory.java | 20 ++-
.../r/install.cran.packages.R | 49 ++++--
mx.fastr/mx_fastr.py | 7 +-
mx.fastr/mx_fastr_pkgs.py | 157 +++++++++++-------
5 files changed, 153 insertions(+), 84 deletions(-)
diff --git a/.gitignore b/.gitignore
index 3eed6ca477..756f43343c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -88,8 +88,8 @@ output.cfg
**/nbproject/**
**/build.xml
/scratch/
-/test/
-/test_gnur/
+/test.fastr/
+/test.gnur/
scratch/
bin/
share/
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/system/ProcessSystemFunctionFactory.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/system/ProcessSystemFunctionFactory.java
index d1f8116fb1..fac23adfb4 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/system/ProcessSystemFunctionFactory.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/system/ProcessSystemFunctionFactory.java
@@ -26,6 +26,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.lang.ProcessBuilder.Redirect;
import java.util.Map;
+import java.util.concurrent.TimeUnit;
import com.oracle.truffle.api.CompilerDirectives.TruffleBoundary;
import com.oracle.truffle.api.frame.VirtualFrame;
@@ -35,6 +36,10 @@ import com.oracle.truffle.r.runtime.data.RDataFactory;
import com.oracle.truffle.r.runtime.data.RStringVector;
public class ProcessSystemFunctionFactory extends SystemFunctionFactory {
+ /**
+ * Temporary support for (test) processes that hang.
+ */
+ private static final String TIMEOUT = "FASTR_PROCESS_TIMEOUT";
@Override
public Object execute(VirtualFrame frame, String command, boolean intern) {
@@ -65,7 +70,20 @@ public class ProcessSystemFunctionFactory extends SystemFunctionFactory {
readThread = new ProcessOutputManager.OutputThreadVariable("system", os);
readThread.start();
}
- rc = p.waitFor();
+ String timeoutVar = System.getenv(TIMEOUT);
+ if (timeoutVar != null) {
+ long timeout;
+ try {
+ timeout = Integer.parseInt(timeoutVar);
+ } catch (NumberFormatException ex) {
+ timeout = 5;
+ }
+ boolean exited = p.waitFor(timeout, TimeUnit.MINUTES);
+ rc = exited ? 0 : 127;
+ } else {
+ rc = p.waitFor();
+ }
+
if (intern) {
// capture output in character vector
String output = new String(readThread.getData(), 0, readThread.getTotalRead());
diff --git a/com.oracle.truffle.r.test.cran/r/install.cran.packages.R b/com.oracle.truffle.r.test.cran/r/install.cran.packages.R
index 8cf210cda4..d38eab1b7d 100644
--- a/com.oracle.truffle.r.test.cran/r/install.cran.packages.R
+++ b/com.oracle.truffle.r.test.cran/r/install.cran.packages.R
@@ -35,7 +35,7 @@
# If unset, defaults to "http://cran.cnr.berkeley.edu/"
# However, a local copy of the CRAN repo can be used either by setting the LOCAL_CRAN_REPO env variable or setting --contrib-url
-# Packages are installed into the directory specified by the --lib arg (or R_LIBS_USER env var)
+# Packages are installed into the directory specified by the --lib arg (or R_LIBS env var)
# Blacklisted packages nor their dependents will not be installed. By default the list of blacklisted
# packages will be read from the file in the --blacklist-file arg or the PACKAGE_BLACKLIST env var.
@@ -46,9 +46,9 @@
# Package: name
# Reason: reason
-# The env var R_LIBS_USER or the option --lib must be set to the directory where the install should take place.
+# The env var R_LIBS or the option --lib must be set to the directory where the install should take place.
# N.B. --lib works for installation. However, when running tests ( --run-tests), it does not and
-# R_LIBS_USER must be set instead (as well) since some of the test code has explicit "library(foo)" calls
+# R_LIBS must be set instead (as well) since some of the test code has explicit "library(foo)" calls
# without a "lib.loc" argument.
# A single package install can be handled in three ways, based on the run-mode argument (default system):
@@ -75,6 +75,8 @@
# TODO At some point this will need to upgraded to support installation from other repos, e.g. BioConductor, github
+# All fatal errors terminate with a return code of 100
+
args <- commandArgs(TRUE)
usage <- function() {
@@ -98,7 +100,7 @@ usage <- function() {
"[--count-daily count]",
"[--ok-only]",
"[--pkg.pattern package-pattern] \n"))
- quit(status=1)
+ quit(status=100)
}
trim <- function (x) gsub("^\\s+|\\s+$", "", x)
@@ -211,7 +213,7 @@ create.blacklist <- function() {
abort <- function(msg) {
print(msg)
- quit("no", 1)
+ quit("no", status=100)
}
set.contriburl <- function() {
@@ -516,6 +518,16 @@ get.blacklist <- function() {
blacklist
}
+show.install.status <- function(test.pkgnames) {
+ if (print.install.status) {
+ cat("BEGIN install status\n")
+ for (pkgname.i in test.pkgnames) {
+ cat(paste0(pkgname.i, ":"), ifelse(install.status[pkgname.i], "OK", "FAILED"), "\n")
+ }
+ cat("END install status\n")
+ }
+}
+
# performs the installation, or logs what it would install if dry.run = T
do.it <- function() {
test.pkgnames <- get.pkgs()
@@ -523,7 +535,7 @@ do.it <- function() {
if (list.versions) {
for (pkgname in test.pkgnames) {
pkg <- toinstall.pkgs[pkgname, ]
- # pretend we are acessing CRAN if list.canonical
+ # pretend we are accessing CRAN if list.canonical
list.contriburl = ifelse(list.canonical, "https://cran.r-project.org/src/contrib", contriburl)
cat(pkg["Package"], pkg["Version"], paste0(list.contriburl, "/", pkgname, "_", pkg["Version"], ".tar.gz"), "\n", sep=",")
}
@@ -533,14 +545,7 @@ do.it <- function() {
cat("BEGIN package installation\n")
install.pkgs(test.pkgnames)
cat("END package installation\n")
-
- if (print.install.status) {
- cat("BEGIN install status\n")
- for (pkgname.i in test.pkgnames) {
- cat(paste0(pkgname.i, ":"), ifelse(install.status[pkgname.i], "OK", "FAILED"), "\n")
- }
- cat("END install status\n")
- }
+ show.install.status(test.pkgnames)
}
if (run.tests) {
@@ -554,6 +559,8 @@ do.it <- function() {
}
matched.pkgnames <- sapply(test.pkgnames, match.fun)
test.pkgnames <- test.pkgnames[matched.pkgnames]
+ # fake the install
+ show.install.status(test.pkgnames)
}
cat("BEGIN package tests\n")
@@ -608,12 +615,18 @@ install.pkg <- function(pkgname) {
return(rc)
}
+gnu_rscript <- function() {
+ rv <- R.Version()
+ dirv <- paste0('R-', rv$major, '.', rv$minor)
+ file.path("com.oracle.truffle.r.native/gnur", dirv, 'bin/Rscript')
+}
+
system.install <- function(pkgname) {
script <- normalizePath("com.oracle.truffle.r.test.cran/r/install.package.R")
if (is.fastr()) {
rscript = file.path(R.home(), "bin", "Rscript")
} else {
- rscript = "Rscript"
+ rscript = gnu_rscript()
}
args <- c(script, pkgname, contriburl, lib.install)
rc <- system2(rscript, args)
@@ -657,7 +670,7 @@ system.test <- function(pkgname) {
if (is.fastr()) {
rscript = file.path(R.home(), "bin", "Rscript")
} else {
- rscript = "Rscript"
+ rscript = gnu_rscript()
}
args <- c(script, pkgname, file.path(testdir, pkgname), lib.install)
rc <- system2(rscript, args)
@@ -794,9 +807,9 @@ cat.args <- function() {
}
check.libs <- function() {
- lib.install <<- Sys.getenv("R_LIBS_USER", unset=NA)
+ lib.install <<- Sys.getenv("R_LIBS", unset=NA)
if (is.na(lib.install)) {
- abort("R_LIBS_USER must be set")
+ abort("R_LIBS must be set")
}
if (!file.exists(lib.install) || is.na(file.info(lib.install)$isdir)) {
abort(paste(lib.install, "does not exist or is not a directory"))
diff --git a/mx.fastr/mx_fastr.py b/mx.fastr/mx_fastr.py
index eb145f15c2..a25ef911eb 100644
--- a/mx.fastr/mx_fastr.py
+++ b/mx.fastr/mx_fastr.py
@@ -515,12 +515,13 @@ def gnu_r(args):
cmd = [join(_gnur_path(), 'R')] + args
return mx.run(cmd, nonZeroIsFatal=False)
-def gnu_rscript(args):
+def gnu_rscript(args, env=None):
'''
- run the internally built GNU Rscript executable'
+ run the internally built GNU Rscript executable
+ env arg is used by pkgtest
'''
cmd = [join(_gnur_path(), 'Rscript')] + args
- return mx.run(cmd, nonZeroIsFatal=False)
+ return mx.run(cmd, nonZeroIsFatal=False, env=env)
def mx_post_parse_cmd_line(opts):
mx_fastr_dists.mx_post_parse_cmd_line(opts)
diff --git a/mx.fastr/mx_fastr_pkgs.py b/mx.fastr/mx_fastr_pkgs.py
index e510aa2264..24d9596cb9 100644
--- a/mx.fastr/mx_fastr_pkgs.py
+++ b/mx.fastr/mx_fastr_pkgs.py
@@ -21,30 +21,69 @@
# questions.
#
-from os.path import join, exists, relpath, dirname
+'''
+The pkgtest command operates in two modes:
+1. In development mode it uses the FastR 'Rscript' command and the internal GNU R for test comparison
+2. In production mode it uses the GraalVM 'Rscript' command and a GNU R loaded as a sibling suite. This is indicated
+by the environment variable 'GRAALVM_FASTR' being set.
+
+Evidently in case 2, there is the potential for a version mismatch between FastR and GNU R, and this is checked.
+
+In either case all the output is placed in the fastr suite dir. Separate directories are used for FastR and GNU R package installs
+and tests, namely 'lib.install.cran.{fastr,gnur}' and 'test.{fastr,gnur}' (sh syntax).
+'''
+from os.path import join, relpath
import shutil, os, re
+import subprocess
import mx
import mx_fastr
quiet = False
+graalvm = None
+
+def _fastr_suite_dir():
+ return mx_fastr._fastr_suite.dir
def _mx_gnur():
return mx.suite('gnur')
-def _create_libinstall(s):
- '''Create lib.install.cran/install.tmp/test for suite s
+def _gnur_rscript():
+ return _mx_gnur().extensions._gnur_rscript_path()
+
+def _graalvm_rscript():
+ assert graalvm is not None
+ return join(graalvm, 'bin', 'Rscript')
+
+def _graalvm():
+ global graalvm
+ if graalvm is None:
+ if os.environ.has_key('GRAALVM_FASTR'):
+ graalvm = os.environ['GRAALVM_FASTR']
+ # version check
+ gnur_version = _mx_gnur().extensions.r_version().split('-')[1]
+ graalvm_version = subprocess.check_output([_graalvm_rscript(), '--version'], stderr=subprocess.STDOUT).rstrip()
+ if not gnur_version in graalvm_version:
+ mx.abort('graalvm R version does not match gnur suite')
+ return graalvm
+
+def _create_libinstall(rvm, test_installed):
'''
- libinstall = join(s.dir, "lib.install.cran")
- # make sure its empty
- shutil.rmtree(libinstall, ignore_errors=True)
- os.mkdir(libinstall)
- install_tmp = join(s.dir, "install.tmp")
+ Create lib.install.cran.<rvm>/install.tmp.<rvm>/test.<rvm> for <rvm>: fastr or gnur
+ If use_installed_pkgs is True, assume lib.install exists and is populated (development)
+ '''
+ libinstall = join(_fastr_suite_dir(), "lib.install.cran." + rvm)
+ if not test_installed:
+ # make sure its empty
+ shutil.rmtree(libinstall, ignore_errors=True)
+ os.mkdir(libinstall)
+ install_tmp = join(_fastr_suite_dir(), "install.tmp." + rvm)
+# install_tmp = join(_fastr_suite_dir(), "install.tmp")
shutil.rmtree(install_tmp, ignore_errors=True)
os.mkdir(install_tmp)
- test = join(s.dir, "test")
- shutil.rmtree(test, ignore_errors=True)
- os.mkdir(test)
- return libinstall, install_tmp
+ testdir = join(_fastr_suite_dir(), "test." + rvm)
+ shutil.rmtree(testdir, ignore_errors=True)
+ os.mkdir(testdir)
+ return libinstall, install_tmp, testdir
def _log_step(state, step, rvariant):
if not quiet:
@@ -63,12 +102,6 @@ def _installpkgs_script():
cran_test = _cran_test_project_dir()
return join(cran_test, 'r', 'install.cran.packages.R')
-def _is_graalvm():
- return os.environ.has_key('GRAALVM_FASTR')
-
-def _graalvm():
- return os.environ['GRAALVM_FASTR']
-
def _installpkgs(args, **kwargs):
'''
Runs the R script that does package/installation and testing.
@@ -77,11 +110,10 @@ def _installpkgs(args, **kwargs):
FastR, but instead have to invoke the command directly.
'''
script = _installpkgs_script()
- if _is_graalvm():
- rscript = join(_graalvm(), 'bin', 'Rscript')
- return mx.run([rscript, script] + args, **kwargs)
- else:
+ if _graalvm() is None:
return mx_fastr.rscript([script] + args, **kwargs)
+ else:
+ return mx.run([_graalvm_rscript(), script] + args, **kwargs)
def pkgtest(args):
@@ -90,12 +122,10 @@ def pkgtest(args):
rc: 0 for success; 1: install fail, 2: test fail, 3: install&test fail
'''
- libinstall, install_tmp = _create_libinstall(mx.suite('fastr'))
+ test_installed = '--no-install' in args
+ fastr_libinstall, fastr_install_tmp, fastr_testdir = _create_libinstall('fastr', test_installed)
+ gnur_libinstall, gnur_install_tmp, gnur_testdir = _create_libinstall('gnur', test_installed)
- if _is_graalvm():
- stacktrace_args = ['-J:-DR:-PrintErrorStacktracesToFile', '-J:-DR:+PrintErrorStacktraces']
- else:
- stacktrace_args = ['--J', '@-DR:-PrintErrorStacktracesToFile -DR:+PrintErrorStacktraces']
if "--quiet" in args:
global quiet
quiet = True
@@ -154,11 +184,15 @@ def pkgtest(args):
if time_match:
pkg_name = time_match.group(1)
test_time = time_match.group(2)
- with open(join('test', pkg_name, 'test_time'), 'w') as f:
+ with open(join(_pkg_testdir('fastr', pkg_name), 'test_time'), 'w') as f:
f.write(test_time)
env = os.environ.copy()
- env["TMPDIR"] = install_tmp
- env['R_LIBS_USER'] = libinstall
+ env["TMPDIR"] = fastr_install_tmp
+ env['R_LIBS'] = fastr_libinstall
+ if not env.has_key('FASTR_PROCESS_TIMEOUT'):
+ env['FASTR_PROCESS_TIMEOUT'] = '5'
+ env['FASTR_OPTION_PrintErrorStacktracesToFile'] = 'false'
+ env['FASTR_OPTION_PrintErrorStacktraces'] = 'true'
# TODO enable but via installing Suggests
#_install_vignette_support('FastR', env)
@@ -167,12 +201,13 @@ def pkgtest(args):
# install and test the packages, unless just listing versions
if not '--list-versions' in install_args:
install_args += ['--run-tests']
+ install_args += ['--testdir', 'test.fastr']
if not '--print-install-status' in install_args:
install_args += ['--print-install-status']
_log_step('BEGIN', 'install/test', 'FastR')
# Currently installpkgs does not set a return code (in install.cran.packages.R)
- rc = _installpkgs(stacktrace_args + install_args, nonZeroIsFatal=False, env=env, out=out, err=out)
+ rc = _installpkgs(install_args, nonZeroIsFatal=False, env=env, out=out, err=out)
if rc == 100:
# fatal error connecting to package repo
mx.abort(rc)
@@ -187,9 +222,9 @@ def pkgtest(args):
install_failure = single_pkg and rc == 1
if '--run-tests' in install_args and not install_failure:
# in order to compare the test output with GnuR we have to install/test the same
- # set of packages with GnuR, which must be present as a sibling suite
+ # set of packages with GnuR
ok_pkgs = [k for k, v in out.install_status.iteritems() if v]
- _gnur_install_test(ok_pkgs)
+ _gnur_install_test(ok_pkgs, gnur_libinstall, gnur_install_tmp)
_set_test_status(out.test_info)
print 'Test Status'
for pkg, test_status in out.test_info.iteritems():
@@ -197,7 +232,11 @@ def pkgtest(args):
rc = rc | 2
print '{0}: {1}'.format(pkg, test_status.status)
- shutil.rmtree(install_tmp, ignore_errors=True)
+ # tar up the test results
+ subprocess.call(['tar', 'cf', join(_fastr_suite_dir, fastr_testdir + '.tar'), os.path.basename(fastr_testdir)])
+ subprocess.call(['tar', 'cf', join(_fastr_suite_dir, gnur_testdir + '.tar'), os.path.basename(gnur_testdir)])
+
+ shutil.rmtree(fastr_install_tmp, ignore_errors=True)
return rc
class TestFileStatus:
@@ -219,11 +258,11 @@ class TestStatus:
self.status = "UNKNOWN"
self.testfile_outputs = dict()
-def _pkg_testdir(suite, pkg_name):
- return join(mx.suite(suite).dir, 'test', pkg_name)
+def _pkg_testdir(rvm, pkg_name):
+ return join(_fastr_suite_dir(), 'test.' + rvm, pkg_name)
-def _get_test_outputs(suite, pkg_name, test_info):
- pkg_testdir = _pkg_testdir(suite, pkg_name)
+def _get_test_outputs(rvm, pkg_name, test_info):
+ pkg_testdir = _pkg_testdir(rvm, pkg_name)
for root, _, files in os.walk(pkg_testdir):
if not test_info.has_key(pkg_name):
test_info[pkg_name] = TestStatus()
@@ -246,44 +285,42 @@ def _get_test_outputs(suite, pkg_name, test_info):
relfile = relpath(absfile, pkg_testdir)
test_info[pkg_name].testfile_outputs[relfile] = TestFileStatus(status, absfile)
-def _install_vignette_support(rvariant, env):
+def _install_vignette_support(rvm, env):
# knitr is needed for vignettes, but FastR can't handle it yet
- if rvariant == 'FastR':
+ if rvm == 'FastR':
return
- _log_step('BEGIN', 'install vignette support', rvariant)
- args = ['--ignore-blacklist', '^rmarkdown$|^knitr$']
- _gnur_installpkgs(args, env)
- _log_step('END', 'install vignette support', rvariant)
-
-def _gnur_installpkgs(args, env, **kwargs):
- return mx.run(['Rscript', _installpkgs_script()] + args, env=env, **kwargs)
+ _log_step('BEGIN', 'install vignette support', rvm)
+ args = [_installpkgs_script(), '--ignore-blacklist', '^rmarkdown$|^knitr$']
+ mx_fastr.gnu_rscript(args, env)
+ _log_step('END', 'install vignette support', rvm)
-def _gnur_install_test(pkgs):
- gnur_packages = join(_mx_gnur().dir, 'gnur.packages')
+def _gnur_install_test(pkgs, gnur_libinstall, gnur_install_tmp):
+ gnur_packages = join(_fastr_suite_dir(), 'gnur.packages')
with open(gnur_packages, 'w') as f:
for pkg in pkgs:
f.write(pkg)
f.write('\n')
- # clone the cran test project into gnur
- gnur_cran_test_project_dir = join(_mx_gnur().dir, _cran_test_project())
- if not exists(gnur_cran_test_project_dir):
- shutil.copytree(_cran_test_project_dir(), gnur_cran_test_project_dir)
- gnur_libinstall, gnur_install_tmp = _create_libinstall(_mx_gnur())
env = os.environ.copy()
- gnur = _mx_gnur().extensions
- path = env['PATH']
- env['PATH'] = dirname(gnur._gnur_rscript_path()) + os.pathsep + path
env["TMPDIR"] = gnur_install_tmp
- env['R_LIBS_USER'] = gnur_libinstall
+ env['R_LIBS'] = gnur_libinstall
# TODO enable but via installing Suggests
# _install_vignette_support('GnuR', env)
- args = ['--pkg-filelist', gnur_packages]
+ args = []
+ if _graalvm():
+ args += [_gnur_rscript()]
+ args += [_installpkgs_script()]
+ args += ['--pkg-filelist', gnur_packages]
args += ['--run-tests']
+ args += ['--run-mode', 'internal']
args += ['--ignore-blacklist']
+ args += ['--testdir', 'test.gnur']
_log_step('BEGIN', 'install/test', 'GnuR')
- _gnur_installpkgs(args, env=env, cwd=_mx_gnur().dir, nonZeroIsFatal=False)
+ if _graalvm():
+ mx.run(args, nonZeroIsFatal=False, env=env)
+ else:
+ mx_fastr.gnu_rscript(args, env=env)
_log_step('END', 'install/test', 'GnuR')
def _set_test_status(fastr_test_info):
--
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