From michael.weylandt at gmail.com  Tue Apr  2 16:21:37 2013
From: michael.weylandt at gmail.com (Michael Weylandt)
Date: Tue, 2 Apr 2013 09:21:37 -0500
Subject: [Rd] [R] Rpy2 and Mac OS X 10.8.3
In-Reply-To: <CADKu8RGGOTj7C3J1ss0QGwBGzGg+hDPeq4zuOk=JK3r4_Ozn5g@mail.gmail.com>
References: <CADKu8RGGOTj7C3J1ss0QGwBGzGg+hDPeq4zuOk=JK3r4_Ozn5g@mail.gmail.com>
Message-ID: <2BE69B71-0354-4EBE-8B1E-95574A954B5F@gmail.com>

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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[Rd] [R] Rpy2 and Mac OS X 10.8.3
Michael Weylandt