Rpy2 and Mac OS X 10.8.3
On Apr 2, 2013, at 9:45 AM, Craig Watson wrote:
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?
Try using valgrind, at a cursory glance this seems like some memory corruption... However, what makes me really uneasy is that you have a lot of conflicting stuff coming from /opt/local -- in particular it seems as if CRAN R and /opt/local is being mixed up - chances are that you are mixing incompatible binaries. Either build everything (incl. R) the way you do in /opt/local or make sure you don't have duplicated incompatible parts in /ipt/local and the framework. Cheers, Simon
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
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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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