def test_parse_log_error(self):
"""Test basic parse_log_for_error functionality."""
errors = ft.parse_log_for_error("error failed", True)
self.assertEqual(len(errors), 1)
# I expect tests to be run from the base easybuild directory
self.assertEqual(os.getcwd(), ft.find_base_dir())
def install_R_package(self, cmd, inp=None):
"""Install R package as specified, and check for errors."""
cmdttdouterr, _ = run_cmd(cmd,
log_all=True,
simple=False,
inp=inp,
regexp=False)
cmderrors = parse_log_for_error(cmdttdouterr, regExp="^ERROR:")
if cmderrors:
cmd = "R -q --no-save"
stdin = """
remove.library(%s)
""" % self.name
# remove package if errors were detected
# it's possible that some of the dependencies failed, but the package itself was installed
run_cmd(cmd,
log_all=False,
log_ok=False,
simple=False,
inp=stdin,
regexp=False)
self.log.error(
"Errors detected during installation of R package %s!" %
self.name)
else:
self.log.debug("R package %s installed succesfully" % self.name)
def test_parse_log_error(self):
"""Test basic parse_log_for_error functionality."""
errors = ft.parse_log_for_error("error failed", True)
self.assertEqual(len(errors), 1)
# I expect tests to be run from the base easybuild directory
self.assertEqual(os.getcwd(), ft.find_base_dir())
def runTest(self):
"""
verify all the possible extract commands
also run_cmd should work with some basic echo/exit combos
"""
cmd = ft.extract_cmd("test.zip")
self.assertEqual("unzip -qq test.zip", cmd)
cmd = ft.extract_cmd("/some/path/test.tar")
self.assertEqual("tar xf /some/path/test.tar", cmd)
cmd = ft.extract_cmd("test.tar.gz")
self.assertEqual("tar xzf test.tar.gz", cmd)
cmd = ft.extract_cmd("test.tgz")
self.assertEqual("tar xzf test.tgz", cmd)
cmd = ft.extract_cmd("test.bz2")
self.assertEqual("bunzip2 test.bz2", cmd)
cmd = ft.extract_cmd("test.tbz")
self.assertEqual("tar xjf test.tbz", cmd)
cmd = ft.extract_cmd("test.tar.bz2")
self.assertEqual("tar xjf test.tar.bz2", cmd)
(out, ec) = ft.run_cmd("echo hello")
self.assertEqual(out, "hello\n")
# no reason echo hello could fail
self.assertEqual(ec, 0)
(out, ec) = ft.run_cmd_qa("echo question", {"question":"answer"})
self.assertEqual(out, "question\n")
# no reason echo hello could fail
self.assertEqual(ec, 0)
self.assertEqual(True, ft.run_cmd("echo hello", simple=True))
self.assertEqual(False, ft.run_cmd("exit 1", simple=True, log_all=False, log_ok=False))
name = ft.convert_name("test+test-test")
self.assertEqual(name, "testplustestmintest")
name = ft.convert_name("test+test-test", True)
self.assertEqual(name, "TESTPLUSTESTMINTEST")
errors = ft.parse_log_for_error("error failed", True)
self.assertEqual(len(errors), 1)
# I expect tests to be run from the base easybuild directory
self.assertEqual(os.getcwd(), ft.find_base_dir())
def install_R_package(self, cmd, inp=None):
"""Install R package as specified, and check for errors."""
cmdttdouterr, _ = run_cmd(cmd, log_all=True, simple=False, inp=inp, regexp=False)
cmderrors = parse_log_for_error(cmdttdouterr, regExp="^ERROR:")
if cmderrors:
cmd = "R -q --no-save"
stdin = """
remove.library(%s)
""" % self.name
# remove package if errors were detected
# it's possible that some of the dependencies failed, but the package itself was installed
run_cmd(cmd, log_all=False, log_ok=False, simple=False, inp=stdin, regexp=False)
self.log.error("Errors detected during installation of R package %s!" % self.name)
else:
self.log.debug("R package %s installed succesfully" % self.name)
