def test_find_onlyfromloadedlibrary():
with pytest.raises(KeyError):
rinterface.globalenv.find('survfit')
try:
rinterface.evalr('library("survival")')
sfit_R = rinterface.globalenv.find('survfit')
assert isinstance(sfit_R, rinterface.SexpClosure)
finally:
rinterface.evalr('detach("package:survival")')
def __repr__(self):
# TODO: hack to work around an issue with calling R functions
# with rpy2 (language objects seem to be evaluated). Without
# the issue, the representation should simply be
# ri.baseenv['deparse'](self)[0]
tmp_r_var = str(uuid.uuid4())
representation = None
try:
ri.globalenv[tmp_r_var] = self
representation = ri.evalr('deparse(`{}`)'.format(tmp_r_var))[0]
finally:
del ri.globalenv[tmp_r_var]
return 'Rlang( {} )'.format(representation)
def test_non_asciil():
u_char = '\u21a7'
b_char = b'\xe2\x86\xa7'
assert (b_char == u_char.encode('utf-8'))
sexp = ri.StrSexpVector((u'\u21a7', ))
char = sexp[0]
assert isinstance(char, str)
# FIXME: the following line is failing on drone, but not locally
assert u'\u21a7'.encode('utf-8') == char.encode('utf-8')
# because of this, the following line is used to pass the test
# until I have more reports from users or manage to reproduce
# myself what is happening on drone.io.
sexp = ri.evalr('c("ěščřžýáíé", "abc", "百折不撓")')
assert all(isinstance(x, str) for x in sexp)
def test_rclass_get():
sexp = rinterface.baseenv.find('character')(1)
assert len(sexp.rclass) == 1
assert sexp.rclass[0] == 'character'
sexp = rinterface.baseenv.find('matrix')(0)
if rinterface.evalr('R.version$major')[0] >= '4':
assert tuple(sexp.rclass) == ('matrix', 'array')
else:
assert tuple(sexp.rclass) == ('matrix', )
sexp = rinterface.baseenv.find('array')(0)
assert len(sexp.rclass) == 1
assert sexp.rclass[0] == 'array'
sexp = rinterface.baseenv.find('new.env')()
assert len(sexp.rclass) == 1
assert sexp.rclass[0] == 'environment'
import array
import pytest
import rpy2.rinterface_lib.sexp
from rpy2 import rinterface
from rpy2 import robjects
@pytest.mark.parametrize(
'cls, values, expected_cls',
[(rinterface.IntSexpVector, (1, 2), robjects.vectors.IntVector),
(rinterface.FloatSexpVector, (1.1, 2.2), robjects.vectors.FloatVector),
(rinterface.StrSexpVector, ('ab', 'cd'), robjects.vectors.StrVector),
(rinterface.BoolSexpVector, (True, False), robjects.vectors.BoolVector),
(rinterface.ByteSexpVector, b'ab', robjects.vectors.ByteVector),
(lambda x: rinterface.evalr(x), 'y ~ x', robjects.Formula)])
def test_sexpvector_to_ro(cls, values, expected_cls):
v_ri = cls(values)
v_ro = robjects.default_converter.rpy2py(v_ri)
assert isinstance(v_ro, expected_cls)
def test_mapperR2Python_function():
sexp = rinterface.globalenv.find('plot')
ob = robjects.default_converter.rpy2py(sexp)
assert isinstance(ob, robjects.Function)
def test_mapperR2Python_environment():
sexp = rinterface.globalenv.find('.GlobalEnv')
assert isinstance(robjects.default_converter.rpy2py(sexp),
robjects.Environment)
# TODO: uuid is used to create a temporary symbol. This is a ugly
# hack to work around an issue with with calling R functions
# (language objects seem to be evaluated when doing so from rpy2
# but not when doing it from R).
import typing
import uuid
from rpy2.robjects import conversion
from rpy2.robjects.robject import RObject
import rpy2.rinterface as ri
_reval = ri.baseenv['eval']
_parse = ri.parse
try:
_str2lang = ri.baseenv['str2lang']
except KeyError:
_str2lang = ri.evalr('function(s) parse(text=s, keep.source=FALSE)[[1]]')
def eval(x: str, envir: ri.SexpEnvironment = ri.globalenv) -> ri.Sexp:
""" Evaluate R code. If the input object is an R expression it
evaluates it directly, if it is a string it parses it before
evaluating it.
By default the evaluation is performed in R's global environment
but a specific environment can be specified.
Args:
x (str): a string to be parsed and evaluated as R code
envir (rpy2.rinterface.SexpEnvironment): An R environment in
which to evaluate the R code.
Returns:
def test_R_to_NAReal():
r_na_real = ri.evalr('NA_real_')[0]
assert math.isnan(r_na_real)
def test_r_to_NAInteger():
na_int = ri.NA_Integer
r_na_int = ri.evalr("NA_integer_")[0]
assert r_na_int is na_int
def test_R_to_NALogical():
r_na_lgl = ri.evalr('NA')[0]
assert r_na_lgl is ri.NA
def test_R_to_NAComplex():
r_na_complex = ri.evalr('NA_complex_')[0]
assert math.isnan(r_na_complex.real)
assert math.isnan(r_na_complex.imag)
def test_r_to_NACharacter():
na_character = ri.NA_Character
r_na_character = ri.evalr("NA_character_")
assert r_na_character.typeof == ri.RTYPES.STRSXP
assert len(r_na_character) == 1
assert r_na_character.get_charsxp(0).rid == na_character.rid
def test_rclass_get_sym():
# issue #749
fit = rinterface.evalr("""
stats::lm(y ~ x, data=base::data.frame(y=1:10, x=2:11))
""")
assert tuple(fit[9].rclass) == ('call', )
