Revision: 621
http://rpy.svn.sourceforge.net/rpy/?rev=621&view=rev
Author: lgautier
Date: 2008-08-08 13:29:24 +0000 (Fri, 08 Aug 2008)
Log Message:
-----------
- Overflow issues on Python 2.4/64 bits when indexing R vector with very large
integers.
- Handling of negative indexes for :class:`SexpVector`'s :meth:`__getitem__`
and :meth:`__setitem__` was missing
Modified Paths:
--------------
branches/rpy_nextgen/NEWS
branches/rpy_nextgen/doc/source/overview.rst
branches/rpy_nextgen/rpy/rinterface/rinterface.c
branches/rpy_nextgen/rpy/rinterface/rinterface.h
branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
Modified: branches/rpy_nextgen/NEWS
===================================================================
--- branches/rpy_nextgen/NEWS 2008-08-07 17:33:42 UTC (rev 620)
+++ branches/rpy_nextgen/NEWS 2008-08-08 13:29:24 UTC (rev 621)
@@ -19,6 +19,16 @@
- :class:`R` remains a singleton, but does not throw an exception when
multiple instances are requested
+Bugs fixed
+----------
+
+- Unable to compile on Python2.4 (definition of aliases to Python2.5-specific
were not where they should be).
+
+- Overflow issues on Python 2.4/64 bits when indexing R vector with very large
integers.
+
+- Handling of negative indexes for :class:`SexpVector`'s :meth:`__getitem__`
and :meth:`__setitem__` was missing
+
+
Release 2.0.0a2
===============
Modified: branches/rpy_nextgen/doc/source/overview.rst
===================================================================
--- branches/rpy_nextgen/doc/source/overview.rst 2008-08-07 17:33:42 UTC
(rev 620)
+++ branches/rpy_nextgen/doc/source/overview.rst 2008-08-08 13:29:24 UTC
(rev 621)
@@ -44,10 +44,6 @@
This is developped with R-2.7.1 and Python-2.5.2.
R-2.8.0-dev is sometimes tested, and it does seem to work well.
-Compatibility with Python 2.4 is expected but it was observed to segfault on
rare occasions
-(and the cause is not yet identified).
-
-
Download
^^^^^^^^
Modified: branches/rpy_nextgen/rpy/rinterface/rinterface.c
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/rinterface.c 2008-08-07 17:33:42 UTC
(rev 620)
+++ branches/rpy_nextgen/rpy/rinterface/rinterface.c 2008-08-08 13:29:24 UTC
(rev 621)
@@ -1237,7 +1237,7 @@
VectorSexp_item(PyObject *object, Py_ssize_t i)
{
PyObject* res;
- R_len_t i_R;
+ R_len_t i_R, len_R;
SEXP *sexp = &(RPY_SEXP((PySexpObject *)object));
if (! sexp) {
@@ -1245,12 +1245,27 @@
return NULL;
}
- /* R is still with int for indexes */
+ /* On 64bits, Python is apparently able to use larger integer
+ * than R for indexing. */
if (i >= R_LEN_T_MAX) {
PyErr_Format(PyExc_IndexError, "Index value exceeds what R can handle.");
res = NULL;
+ return;
}
- else if (i >= GET_LENGTH(*sexp)) {
+
+ len_R = GET_LENGTH(*sexp);
+
+ if (i < 0) {
+ i = len_R - i;
+ }
+
+ if (i < 0) {
+ PyErr_Format(PyExc_IndexError,
+ "Mysterious error: likely an integer overflow.");
+ res = NULL;
+ return;
+ }
+ if ((i >= GET_LENGTH(*sexp))) {
PyErr_Format(PyExc_IndexError, "Index out of range.");
res = NULL;
}
@@ -1302,16 +1317,22 @@
static int
VectorSexp_ass_item(PyObject *object, Py_ssize_t i, PyObject *val)
{
- R_len_t i_R;
+ R_len_t i_R, len_R;
- /* R is still with int for indexes */
+ /* Check for 64 bits platforms */
if (i >= R_LEN_T_MAX) {
PyErr_Format(PyExc_IndexError, "Index value exceeds what R can handle.");
return -1;
}
SEXP *sexp = &(RPY_SEXP((PySexpObject *)object));
- if (i >= GET_LENGTH(*sexp)) {
+ len_R = GET_LENGTH(*sexp);
+
+ if (i < 0) {
+ i = len_R - i;
+ }
+
+ if (i >= len_R) {
PyErr_Format(PyExc_IndexError, "Index out of range.");
return -1;
}
Modified: branches/rpy_nextgen/rpy/rinterface/rinterface.h
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/rinterface.h 2008-08-07 17:33:42 UTC
(rev 620)
+++ branches/rpy_nextgen/rpy/rinterface/rinterface.h 2008-08-08 13:29:24 UTC
(rev 621)
@@ -7,6 +7,8 @@
/* Back-compatibility with Python 2.4 */
#if (PY_VERSION_HEX < 0x02050000)
+#define PY_SSIZE_T_MAX INT_MAX
+#define PY_SSIZE_T_MIN INT_MIN
typedef int Py_ssize_t;
typedef inquiry lenfunc;
typedef intargfunc ssizeargfunc;
Modified: branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
2008-08-07 17:33:42 UTC (rev 620)
+++ branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
2008-08-08 13:29:24 UTC (rev 621)
@@ -108,6 +108,14 @@
self.assertTrue(idem(mySeq, myList[0]))
self.assertTrue(idem(letters_R, myList[1]))
+ letters_R = ri.globalEnv.get("letters")
+ self.assertEquals('z', letters_R[-1])
+
+ def testGetItemNegativeOutOfBound(self):
+ letters_R = ri.globalEnv.get("letters")
+ self.assertRaises(IndexError, letters_R.__getitem__,
+ -100)
+
def testGetItemOutOfBound(self):
myVec = ri.SexpVector([0, 1, 2, 3, 4, 5], ri.INTSXP)
self.assertRaises(IndexError, myVec.__getitem__, 10)
@@ -118,10 +126,9 @@
def testAssignItemDifferentType(self):
c_R = ri.globalEnv.get("c")
myVec = c_R(ri.SexpVector([0, 1, 2, 3, 4, 5], ri.INTSXP))
- #import pdb; pdb.set_trace()
self.assertRaises(ValueError, myVec.__setitem__, 0,
ri.SexpVector(["a", ], ri.STRSXP))
-
+
def testAssignItemOutOfBound(self):
c_R = ri.globalEnv.get("c")
myVec = c_R(ri.SexpVector([0, 1, 2, 3, 4, 5], ri.INTSXP))
@@ -137,6 +144,9 @@
myVec[3] = ri.SexpVector([100, ], ri.INTSXP)
self.assertTrue(myVec[3] == 100)
+ myVec[-1] = ri.SexpVector([200, ], ri.INTSXP)
+ self.assertTrue(myVec[5] == 200)
+
def testAssignItemReal(self):
c_R = ri.globalEnv.get("c")
myVec = c_R(ri.SexpVector([0.0, 1.0, 2.0, 3.0, 4.0, 5.0],
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