bus error with R 2.12.0

Issue #59 resolved
telliott99 created an issue

An upgrade to R 2.12.0 crashes Python with RPy

from rpy2 import robjects

Bus error

Moving to R 2.11.1 fixed it for a while, but then it came back.

Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin

OS X 10.6.5

R version 2.11.1 (2010-05-31)

R version 2.12.0 (2010-05-31)

details here http://telliott99.blogspot.com/2010/11/i-upgraded-to-r-version-2.html

Comments (5)

  1. Laurent Gautier
    • changed status to open
    • changed milestone to 2.1.9

    Things appear(ed) to be working on OS X 10.5, but I have not tested on 10.6. I have seen segfaults with Python 2.7 or 3.1 on OS X 10.5.

    Try running this with Python version compiled with the debug flag, or through gdb. I can only look into what might be happening with more details.

    In the meanwhile Linux remains the best platform to run rpy2 on.

  2. telliott99 reporter

    Three observations that suggest it's something about my installation:

    • I got the same behavior with R 2.10.1 and R 2.11.1 as with R 2.12.0, even though I've used RPy 2.1.8 fine with R 2.10.1 on my other machines with OS X.
    • After changing the default R to the earlier R versions, I was initially able to work for a while before the crash occurred. Thereafter it always occurs on first import of rpy2.
    • I built Python 2.6.6 with debug enabled, and haven't seen any problem, though it occurs to me that I haven't gone back and tested R 2.12.0 again yet.

    So, it seems that if it is a bug, it's something specific to this installation that's not seen with Python 2.6.6.*

  3. Former user Account Deleted

    I encountered this exact same thing. I believe the issue is with the stock apple python2.6 installation. I can use the python 2.6 install from fink with no problems.

    It is even more mysterious because, even with the problematic osx default python importing rpy2, ie 'from rpy2.robjects import r' works just fine the very first time. If you then Ctrl-d python, start python back up and then try to import you get a bus error. Deleting the egg and then reinstalling with easy_install allows you to import rpy2 once again, for one time only, then you are back to bus errors.

    I included the crash report with a stack trace perhaps it will help.

    Process: Python [31592] Path: /System/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python Identifier: Python Version: ??? (???) Code Type: X86 (Native) Parent Process: bash [318]

    PlugIn Path: /Users/babs/.python-eggs/rpy2-2.1.9_20101127-py2.6-macosx-10.6-universal.egg-tmp/rpy2/rinterface/rinterface.so PlugIn Identifier: rinterface.so PlugIn Version: ??? (???)

    Date/Time: 2010-11-27 18:35:44.773 -0600 OS Version: Mac OS X 10.6.4 (10F569) Report Version: 6

    Interval Since Last Report: 2206403 sec Crashes Since Last Report: 97 Per-App Crashes Since Last Report: 13 Anonymous UUID: 80A96787-082D-49AA-847A-CB474B05816E

    Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000050 Crashed Thread: 0 Dispatch queue: com.apple.main-thread

    Thread 0 Crashed: Dispatch queue: com.apple.main-thread 0 org.python.python 0x0000f922 PyNumber_Int + 101 1 rinterface.so 0x00775cd0 VectorSexp_init + 699 2 org.python.python 0x000504d3 PyType_IsSubtype + 634 3 org.python.python 0x000207dd PyDictProxy_New + 196 4 org.python.python 0x0000c6e0 PyObject_Call + 101 5 org.python.python 0x0008c812 PyEval_EvalFrameEx + 21639 6 org.python.python 0x0008cf74 PyEval_EvalCodeEx + 1720 7 org.python.python 0x0002ee0c PyClassMethod_New + 1823 8 org.python.python 0x0000c6e0 PyObject_Call + 101 9 org.python.python 0x0001c10d PyClass_New + 1603 10 org.python.python 0x0000c6e0 PyObject_Call + 101 11 org.python.python 0x00053d8a _PyType_Lookup + 5617 12 org.python.python 0x00055bc1 PyType_GenericAlloc + 3133 13 org.python.python 0x0000c6e0 PyObject_Call + 101 14 org.python.python 0x0008c812 PyEval_EvalFrameEx + 21639 15 org.python.python 0x0008cf74 PyEval_EvalCodeEx + 1720 16 org.python.python 0x0002ee0c PyClassMethod_New + 1823 17 org.python.python 0x0000c6e0 PyObject_Call + 101 18 org.python.python 0x0001c10d PyClass_New + 1603 19 org.python.python 0x0000c6e0 PyObject_Call + 101 20 org.python.python 0x00053d8a _PyType_Lookup + 5617 21 org.python.python 0x00055bc1 PyType_GenericAlloc + 3133 22 org.python.python 0x0000c6e0 PyObject_Call + 101 23 org.python.python 0x0008c812 PyEval_EvalFrameEx + 21639 24 org.python.python 0x0008cf74 PyEval_EvalCodeEx + 1720 25 org.python.python 0x0008d019 PyEval_EvalCode + 87 26 org.python.python 0x0009a542 PyImport_ExecCodeModuleEx + 240 27 org.python.python 0x000c6576 initzipimport + 6643 28 org.python.python 0x0000c6e0 PyObject_Call + 101 29 org.python.python 0x0000cc6f PyObject_CallMethodObjArgs + 257 30 org.python.python 0x0000efda PyObject_CallMethod + 203 31 org.python.python 0x0009c1c8 _PyImport_FindModule + 1120 32 org.python.python 0x0009c88f PyImport_ReloadModule + 1392 33 org.python.python 0x0009cce7 PyImport_ReloadModule + 2504 34 org.python.python 0x0009d2cb PyImport_ImportModuleLevel + 1221 35 org.python.python 0x0008578f _PyBuiltin_Init + 14665 36 org.python.python 0x0000c6e0 PyObject_Call + 101 37 org.python.python 0x0008678a PyEval_CallObjectWithKeywords + 171 38 org.python.python 0x0008a758 PyEval_EvalFrameEx + 13261 39 org.python.python 0x0008cf74 PyEval_EvalCodeEx + 1720 40 org.python.python 0x0008d019 PyEval_EvalCode + 87 41 org.python.python 0x000a40af Py_CompileString + 111 42 org.python.python 0x000a6134 PyRun_InteractiveOneFlags + 483 43 org.python.python 0x000a6282 PyRun_InteractiveLoopFlags + 216 44 org.python.python 0x000a630b PyRun_AnyFileExFlags + 85 45 org.python.python 0x000b315c Py_Main + 3074 46 org.python.python.app 0x00001eb5 start + 53

    Thread 1: Dispatch queue: com.apple.libdispatch-manager 0 libSystem.B.dylib 0x92b33942 kevent + 10 1 libSystem.B.dylib 0x92b3405c _dispatch_mgr_invoke + 215 2 libSystem.B.dylib 0x92b33519 _dispatch_queue_invoke + 163 3 libSystem.B.dylib 0x92b332be _dispatch_worker_thread2 + 240 4 libSystem.B.dylib 0x92b32d41 _pthread_wqthread + 390 5 libSystem.B.dylib 0x92b32b86 start_wqthread + 30

    Thread 2: 0 libSystem.B.dylib 0x92b329d2 workq_kernreturn + 10 1 libSystem.B.dylib 0x92b32f68 _pthread_wqthread + 941 2 libSystem.B.dylib 0x92b32b86 start_wqthread + 30

    Thread 0 crashed with X86 Thread State (32-bit): eax: 0x00779800 ebx: 0x0000f8d1 ecx: 0x00000000 edx: 0x00000008 edi: 0x00162908 esi: 0x001800f0 ebp: 0xbfffd188 esp: 0xbfffd150 ss: 0x0000001f efl: 0x00010202 eip: 0x0000f922 cs: 0x00000017 ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 cr2: 0x00000050

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(???) <B99607FC-5646-32C8-2C16-AFB5EA9097C2> /usr/lib/liblangid.dylib 0x99299000 - 0x99341ffb com.apple.QD 3.35 (???) <B80B64BC-958B-DA9E-50F9-D7E8333CC5A2> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD 0x9944d000 - 0x9945bfe7 libz.1.dylib 1.2.3 (compatibility 1.0.0) <3CE8AA79-F077-F1B0-A039-9103A4A02E92> /usr/lib/libz.1.dylib 0x9945c000 - 0x99468ff7 libkxld.dylib ??? (???) <322A4B52-8305-3081-6B74-813C3A87A56D> /usr/lib/system/libkxld.dylib 0x998fb000 - 0x9993fff3 com.apple.coreui 2 (114) <29F8F1A4-1C96-6A0F-4CC2-9B85CF83209F> /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI 0xffff0000 - 0xffff1fff libSystem.B.dylib ??? (???) <3441F338-2218-6D36-3F95-3A16FBF6713D> /usr/lib/libSystem.B.dylib

    Model: MacBookPro1,1, BootROM MBP11.0055.B08, 2 processors, Intel Core Duo, 2 GHz, 1 GB, SMC 1.2f10 Graphics: ATI Radeon X1600, ATY,RadeonX1600, PCIe, 256 MB Memory Module: global_name AirPort: spairport_wireless_card_type_airport_extreme (0x168C, 0x86), Atheros 5424: 2.0.19.10 Bluetooth: Version 2.3.3f8, 2 service, 19 devices, 1 incoming serial ports Network Service: AirPort, AirPort, en1 Serial ATA Device: FUJITSU MHV2100BH, 93.16 GB Parallel ATA Device: MATSHITADVD-R UJ-857, 7.24 GB USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8501, 0xfd400000 USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x0217, 0x1d200000 USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8240, 0x5d200000 USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8205, 0x7d100000

  4. Laurent Gautier

    Does the fink-compiled / self-compiled Python have readline support ? There might be a link with #10.

    The "works once per install" bit is quite odd. A wild guess here could be that caching of some sort taking place ? OS X is based on BSD, and a difference at that level would make it only work on Linux. Is there anyone with BSD to report how things are working with it ?

  5. Former user Account Deleted

    If it helps, the bus error actually occurs in rinterface.initr()

    import rpy2.rinterface
    rpy2.rinterface.rinterface.initr()
    Bus error
    
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