[Rd] [R] Rpy2 and Mac OS X 10.8.3
Michael Weylandt
michael.weylandt at gmail.com
Tue Apr 2 16:21:37 CEST 2013
Moving to the more on topic R-devel list.
On Apr 2, 2013, at 2:14, Craig Watson <craig.o.watson at gmail.com> 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?
Almost certainly in rpy2 because library('zoo') is just fine on the R side. Don't have rpy2 around to play further. Have you tried contacting the maintainer directly?
Michael
>
> 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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>
> 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
>
> [[alternative HTML version deleted]]
>
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