I am still experiencing problems (segfault) in pymvpa with rpy2 on 64bit. But
lets start with unittests -- if I try using nosetests to discover/run them then
I can get a segfault too:
1. probably R issue, not RPy2 -- but wanted to check with you:
,---
| $> MVPA_SEED=1 PYTHONPATH=/home/yoh/proj/rpy2/build/lib.linux-x86_64-2.6:$PWD
/usr/bin/python2.6 /usr/bin/nosetests -s -v rpy2
| ...
| TypeError: clip() takes exactly 1 argument (5 given)
| NotImplementedError: Device mode not implemented.
| ok
| testSize (rpy2.rinterface.tests.test_Device.ConcreteDeviceTestCase) ...
done.
| ERROR
| testChooseFileWithError
(rpy2.rinterface.tests.test_EmbeddedR.CallbacksTestCase) ... Error in function
(new = FALSE) : file choice cancelled
| zsh: segmentation fault MVPA_SEED=1
PYTHONPATH=/home/yoh/proj/rpy2/build/lib.linux-x86_64-2.6:$PWD
`---
so segfault again but probably is different from ours in pymvpa (yet to
provide details): while running via nosetests R complaints a lot "Device mode
not implemented", and then segfault seems to fit the "bill":
NotImplementedError: Device deactivation not implemented.
NotImplementedError: Device activation not implemented.
done.
ok
testCanGenKeybd (rpy2.rinterface.tests.test_Device.AbstractDeviceTestCase) ...
==26349== Invalid read of size 8
==26349== at 0x9293B84: GEaddDevice (devices.c:451)
==26349== by 0x9293C0D: GEaddDevice2 (devices.c:501)
==26349== by 0xFF8993A: GrDev_init (rpy_device.c:1252)
==26349== by 0x484EF3: type_call (typeobject.c:742)
==26349== by 0x425FE4: PyObject_Call (abstract.c:2492)
==26349== by 0x4D1692: do_call (ceval.c:3946)
==26349== by 0x4D0A10: call_function (ceval.c:3751)
==26349== by 0x4CB91E: PyEval_EvalFrameEx (ceval.c:2411)
==26349== by 0x4D0D0D: fast_function (ceval.c:3814)
==26349== by 0x4D09EE: call_function (ceval.c:3749)
==26349== by 0x4CB91E: PyEval_EvalFrameEx (ceval.c:2411)
==26349== by 0x4CE0C5: PyEval_EvalCodeEx (ceval.c:2990)
==26349== Address 0xcb1f750 is 256 bytes inside a block of size 488 free'd
==26349== at 0x4C21DBC: free (vg_replace_malloc.c:325)
==26349== by 0x4649EB: PyObject_Free (obmalloc.c:1125)
==26349== by 0x464E27: _PyObject_DebugFree (obmalloc.c:1381)
==26349== by 0x46360C: PyMem_Free (object.c:2287)
==26349== by 0xFF88B9B: GrDev_dealloc (rpy_device.c:705)
==26349== by 0x4632F2: _Py_Dealloc (object.c:2198)
==26349== by 0x59C2F0: frame_dealloc (frameobject.c:420)
==26349== by 0x4632F2: _Py_Dealloc (object.c:2198)
==26349== by 0x4D0D7E: fast_function (ceval.c:3816)
==26349== by 0x4D09EE: call_function (ceval.c:3749)
==26349== by 0x4CB91E: PyEval_EvalFrameEx (ceval.c:2411)
==26349== by 0x4D0D0D: fast_function (ceval.c:3814)
(gdb) p oldd
$2 = (pGEDevDesc) 0xcb1f660
*(gdb) p *oldd
$3 = {dev = 0xdbdbdbdbdbdbdbdb, displayListOn = 3688618971, displayList =
0xdbdbdbdbdbdbdbdb, DLlastElt = 0xdbdbdbdbdbdbdbdb, savedSnapshot =
0xdbdbdbdbdbdbdbdb, dirty = 3688618971, recordGraphics = 3688618971, gesd =
{0xdbdbdbdbdbdbdbdb <repeats 24 times>}, ask = 3688618971}
*(gdb) p *oldd->dev
Cannot access memory at address 0xdbdbdbdbdbdbdbdb
and that happens in
/home/yoh/proj/rpy2/build-dbg/lib/python2.6/site-packages/rpy2/rinterface/tests/test_Device.py
(11): setUp
self.gd = rdevice.GraphicalDevice()
so -- it accesses the address in 'freed' space, and probably it isn't the RPy2
issue, right?
2. minor (probably safe but would be great to have it cleaner)
,---
| $> MVPA_SEED=1 PYTHONPATH=/home/yoh/proj/rpy2/build/lib.linux-x86_64-2.6:$PWD
/usr/bin/python2.6 /usr/bin/nosetests -s -v rpy2.rinterface.tests.test_EmbeddedR
| testChooseFileWithError
(rpy2.rinterface.tests.test_EmbeddedR.CallbacksTestCase) ... Error in function
(new = FALSE) : file choice cancelled
| ok
| ...
| testInterruptR (rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase) ...
Traceback (most recent call last):
| File "/home/yoh/.tmp/tmp5rdj4w.py", line 1, in <module>
| import rpy2.robjects as ro
| File
"/home/yoh/proj/rpy2/build/lib.linux-x86_64-2.6/rpy2/robjects/__init__.py",
line 20, in <module>
| from rpy2.robjects.methods import RS4
| File
"/home/yoh/proj/rpy2/build/lib.linux-x86_64-2.6/rpy2/robjects/methods.py", line
9, in <module>
| quiet = rinterface.BoolSexpVector((True, )))
| ValueError: The first parameter must be a tuple.
| ok
| testSet_initoptions (rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
... ok
| testStr_typeint (rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase) ...
ok
| ...
`---
although tests reported to pass -- so not sure if that spit out traceback is a
'feature' or just somehow missed? (it is also "visible" with using python2.6 -m
rpy2.tests to run the tests)
On Sun, 11 Apr 2010, Laurent wrote:
> I have a rather limited set of complains, so I am thinking that this is
> somehow ready for a release.
> I will have a last check at things, but better if I am not the only one
> looking at it.
> Please report:
> - bugs
> - missing features (advertised in the documentation, or that should
> implicitly be present)
> note: no win32/win64 support at this time, unless I a contributor steps
> forward.
> Thanks,
> Laurent
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