I am having a strange problem. I have been using python + rpy2 on my Mac
for quite sometime now. I recently upgraded to OS X 10.8 from 10.6 and
that's when the problem began.
Now, when I try to load some R packages (like zoo) using robjects.r, python
crashes with seg fault 11. Here's an example below:
>> import rpy2.robjects as ro
>> ro.r(''' library(zoo) ''')
This results in the following crash report (see below). Can anyone help me
debug this and figure out what the problem is?
Thanks!
_________________________________________________________________________________________________________________________
Process: Python [365]
Path:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.3 (2.7.3)
Code Type: X86-64 (Native)
Parent Process: bash [325]
User ID: 501
Date/Time: 2013-04-02 02:55:03.684 -0400
OS Version: Mac OS X 10.8.3 (12D78)
Report Version: 10
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000018
VM Regions Near 0x18:
-->
__TEXT 0000000100000000-0000000100001000 [ 4K]
r-x/rwx SM=COW
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libR.dylib 0x0000000104aeb1c7 GetNewPage + 183
(memory.c:806)
1 libR.dylib 0x0000000104aec44b Rf_allocVector + 2235
(memory.c:2221)
2 libR.dylib 0x0000000104a0816e
get_package_CEntry_table + 174 (Rinlinedfuns.h:513)
3 libR.dylib 0x0000000104a0825f R_RegisterCCallable +
31 (Rdynload.c:1391)
4 zoo.so 0x00000001035e5466 R_init_zoo + 70
(init.c:46)
5 libR.dylib 0x0000000101007089 AddDLL + 201
6 libR.dylib 0x000000010100737a do_dynload + 170
7 libR.dylib 0x00000001010a6aab bcEval + 10043
8 ??? 0x00007fff5fbf4bb0 0 + 140734799760304
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0xffffffff1fffffff rcx: 0x0000000104039608
rdx: 0x0000000104039608
rdi: 0x0000000020000000 rsi: 0x0000000000000000 rbp: 0x00007fff5fbf4240
rsp: 0x00007fff5fbf4210
r8: 0x0000000000000160 r9: 0x0000000000000000 r10: 0x0000000104cf3970
r11: 0x0000000000000000
r12: 0x0000000104cf3830 r13: 0x0000000000000028 r14: 0x0000000000000030
r15: 0x0000000000000001
rip: 0x0000000104aeb1c7 rfl: 0x0000000000010202 cr2: 0x0000000000000018
Logical CPU: 1
Binary Images:
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2004-2012 Python Software Foundation. - 2.7.3)
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External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 178
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=101.2M resident=52.1M(51%)
swapped_out_or_unallocated=49.1M(49%)
Writable regions: Total=48.0M written=32.9M(69%) resident=34.6M(72%)
swapped_out=0K(0%) unallocated=13.3M(28%)
REGION TYPE VIRTUAL
=========== =======
MALLOC 37.8M
MALLOC guard page 32K
STACK GUARD 56.0M
Stack 8192K
VM_ALLOCATE 4K
__DATA 3496K
__LINKEDIT 55.9M
__TEXT 45.4M
__UNICODE 544K
shared memory 12K
=========== =======
TOTAL 207.0M
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