def testSetFlushConsole(self):
flush = {'count': 0}
def f():
flush['count'] = flush['count'] + 1
rinterface.setFlushConsole(f)
self.assertEquals(rinterface.getFlushConsole(), f)
rinterface.baseNameSpaceEnv.get("flush.console")()
self.assertEquals(1, flush['count'])
rinterface.setWriteConsole(rinterface.consoleFlush)
def testSetWriteConsole(self):
buf = []
def f(x):
buf.append(x)
rinterface.setWriteConsole(f)
self.assertEquals(rinterface.getWriteConsole(), f)
code = rinterface.SexpVector(["3", ], rinterface.STRSXP)
rinterface.baseNameSpaceEnv["print"](code)
self.assertEquals('[1] "3"\n', str.join('', buf))
def testWriteConsoleWithError(self):
if sys.version_info[0] == 2 and sys.version_info[1] < 6:
self.assertTrue(False) # cannot be tested with Python < 2.6
return None
def f(x):
raise Exception("Doesn't work.")
rinterface.setWriteConsole(f)
outfile = tempfile.NamedTemporaryFile(mode = 'w',
delete=False)
stderr = sys.stderr
sys.stderr = outfile
try:
code = rinterface.SexpVector(["3", ], rinterface.STRSXP)
rinterface.baseNameSpaceEnv["print"](code)
except Exception, e:
sys.stderr = stderr
raise e
def test_r_import(self):
try:
import rpy2.robjects as robjects
import rpy2.rinterface as rinterface
import rpy2.robjects.numpy2ri
# some tests
x = robjects.r['pi']
v = robjects.FloatVector([1.1, 2.2, 3.3, 4.4, 5.5, 6.6])
m = robjects.r['matrix'](v, nrow=2)
has_R_version = True
version = '%s.%s' % (robjects.r['version'][5][0],
robjects.r['version'][6][0])
except:
has_R_version = False
msg = 'R installation not found.\n\n'\
'To use HMM error correction or plotting functions '\
'R >= Version 2.9 must be installed together with these.'\
'packages:\n'
msg += ', '.join(R_LIBRARIES)
msg += '\n\nSee http://www.r-project.org\n\n'
critical(self, 'R installation not found', info=msg, detail_tb=True)
if has_R_version:
missing_libs = []
buffer = []
rinterface.setWriteConsole(lambda x: buffer.append(x))
for lib_name in R_LIBRARIES:
try:
robjects.r['library'](lib_name)
except:
missing_libs.append(lib_name)
rinterface.setWriteConsole(None)
if len(missing_libs) > 0:
msg = 'Missing R package(s)\n\n'
msg += ', '.join(missing_libs)
msg += '\n\nSee http://www.r-project.org\n\n'
msg += '\n'.join(buffer)
critical(self, 'Missing R libraries', info=msg, detail_tb=True)
qApp.valid_R_version = False
else:
qApp.valid_R_version = True
m = e.args[0].partition("eval(expr, envir, enclos) : ")[2]
if m:
raise TranslatedRRuntimeError("Error: " + m)
else:
raise TranslatedRRuntimeError(*e.args)
visible = visible[0]
if visible:
return result
# There are various possibilities:
# * An error can be raised in parsing or evaling. We try to translate back
# to the R error message, and show it.
# * The command may have a visible return value, e.g. "5 + 4", or not,
# e.g. "a <- 1"
# * The command may cause output to the console, e.g. "print(1:4)".
consolebuffer = []
setWriteConsole(consolebuffer.append)
def Rconsoleexec(command):
try:
res = Rexec(command)
except RRuntimeError as e:
out = e.args[0]
else:
out = ""
if consolebuffer:
out += "".join(consolebuffer)
if res:
out += str(res) + "\n"
del consolebuffer[:]
return out
def tearDown(self):
rinterface.setWriteConsole(rinterface.consolePrint)
rinterface.setReadConsole(rinterface.consoleRead)
rinterface.setReadConsole(rinterface.consoleFlush)