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:
       0x100000000 -        0x100000fff +org.python.python (2.7.3 - 2.7.3)
<6729542A-9233-A64E-2797-4BAF23C0C942>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
       0x100003000 -        0x10016bfe7 +org.python.python (2.7.3, [c]
2004-2012 Python Software Foundation. - 2.7.3)
<35145595-A1C0-45F9-D397-C603EE0E0B54>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python
       0x1002ee000 -        0x1002f3fff +array.so (???)
<5016C2F6-BC06-2B3A-C0C3-CCA546066A73>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/array.so
       0x1002fb000 -        0x1002fcfff +_hashlib.so (???)
<D8332168-1C08-96B7-4ADD-FF44E32E6320>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_hashlib.so
       0x1004b0000 -        0x1004e4ff7 +readline.so (???)
<10B242AB-3587-74AC-3ED9-ADE7AE715FDE>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/readline/readline.so
       0x1004ff000 -        0x100545ff7 +libncurses.5.dylib (5)
<0BA1D173-3328-C80F-0080-770D3A589FF5> /opt/local/lib/libncurses.5.dylib
       0x100582000 -        0x100589ff7 +itertools.so (???)
<A2FF86BD-392B-1694-7585-FC3021FD4915>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/itertools.so
       0x100594000 -        0x1005a3ff7 +_rinterface.so (???)
<9AD185A0-A567-1D9E-5946-94D22301A7E1>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/rinterface/_rinterface.so
       0x1005b5000 -        0x1005e1fff +libRblas.dylib (0)
<79B7884F-707F-3D59-AF76-3C47FF7F7309> /opt/local/lib/*/libRblas.dylib
       0x1005e4000 -        0x1005efff7 +libgomp.1.dylib (2)
<5F6F59F5-49D2-32E5-8E1B-845E24643116> /opt/local/lib/*/libgomp.1.dylib
       0x1005fb000 -        0x1005fcfff +_random.so (???)
<AAC611D8-D82E-4227-27C0-ACD9589D548C>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_random.so
       0x100700000 -        0x100729fff +libreadline.6.2.dylib (6.2)
<E37FDE3E-AE96-525A-DD7C-5444A08C2F30> /opt/local/lib/libreadline.6.2.dylib
       0x10073f000 -        0x10075ffef +liblzma.5.dylib (6.4)
<2436EADC-ADA7-800F-87BE-480E010827C4> /opt/local/lib/liblzma.5.dylib
       0x100765000 -        0x100778fef +libgcc_s.1.dylib (1)
<9521B0A3-DFB2-30E5-81D1-B6FE12351BF2> /opt/local/lib/*/libgcc_s.1.dylib
       0x1007c7000 -        0x1007ccfef +math.so (???)
<E6B861CF-FF7B-01E7-C873-5CCC030C1CE3>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/math.so
       0x1007d3000 -        0x1007d6fef +binascii.so (???)
<7C14C92D-B218-F27F-4F3A-9809AFAB395A>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/binascii.so
       0x1007da000 -        0x1007ecff7 +libz.1.dylib (1.2.7)
<CB0AF5A1-4847-4398-FBE4-78483C8F8866> /opt/local/lib/libz.1.dylib
       0x1007f0000 -        0x1007f1fff +cStringIO.so (???)
<AE22963C-AD85-3017-3AAA-191802F249C6>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/cStringIO.so
       0x1007f6000 -        0x1007f7ff7 +fcntl.so (???)
<328E9F46-8B49-5C09-60B7-E3CD93379EE4>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/fcntl.so
       0x1007fa000 -        0x1007fdfff +lattice.so (0)
<5C6431FB-5B8A-A18A-8018-45A4F96C892D>
/Library/Frameworks/R.framework/Versions/2.15/Resources/library/lattice/libs/x86_64/lattice.so
       0x101000000 -        0x1012e1ff7 +libR.dylib (2.15.3)
<20498FF7-3019-355C-BF42-6C27DFC8CBB4> /opt/local/lib/*/libR.dylib
       0x1013c3000 -        0x10155bfef +libRlapack.dylib (2.15.3)
<B02DC98C-CAC5-3CD1-BF9E-0E47A1ED8831> /opt/local/lib/*/libRlapack.dylib
       0x101564000 -        0x101644fef +libgfortran.3.dylib (4)
<A7BD0581-0B86-399F-A645-6DB5A87F416C> /opt/local/lib/*/libgfortran.3.dylib
       0x10169d000 -        0x10179bfef +libiconv.2.dylib (8.1)
<065A36D7-5F15-7B4C-C3F4-D9B23DFC36A3> /opt/local/lib/libiconv.2.dylib
       0x1017a9000 -        0x1018cfff7 +libicuuc.49.dylib (49.1.2)
<0F420069-D07F-0465-C2F3-A5BA51E4FE35> /opt/local/lib/libicuuc.49.dylib
       0x101932000 -        0x101ac7ff7 +libicui18n.49.dylib (49.1.2)
<BAC093EA-12B8-5A95-7C4D-95217F78680F> /opt/local/lib/libicui18n.49.dylib
       0x101b7c000 -        0x102c9bff7 +libicudata.49.dylib (49.1.2)
<2AE5D81A-8E82-9BDF-3514-B94940A00CB3> /opt/local/lib/libicudata.49.dylib
       0x102c9d000 -        0x102cf1ff7 +libssl.1.0.0.dylib (1)
<5955F68C-357C-A2E8-59F3-D20D85403AB3> /opt/local/lib/libssl.1.0.0.dylib
       0x102d0c000 -        0x102e71ff7 +libcrypto.1.0.0.dylib (1)
<99B0CA7E-26BF-0EEA-FF9A-9516FA2EF3B6> /opt/local/lib/libcrypto.1.0.0.dylib
       0x1031d7000 -        0x1031ddfff +methods.so (0)
<A79F5BAA-658A-3474-B4ED-6D32BB6DE9DE> /opt/local/lib/*/methods.so
       0x10356e000 -        0x103598fef +grDevices.so (0)
<843E2588-8755-320E-88E7-B18BFD55F5DB> /opt/local/lib/*/grDevices.so
       0x1035dc000 -        0x1035defff +time.so (???)
<CA2CD6C7-8CDD-87EB-9327-C05753093B32>
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/time.so
       0x1035e3000 -        0x1035e6ff7 +zoo.so (0)
<5D2C0F1A-C14A-F98D-D67C-1501DD27AEAB>
/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zoo/libs/x86_64/zoo.so
       0x103700000 -        0x103765ff7 +stats.so (0)
<CAF8A6F0-8339-33F6-9054-9A77DD83A867> /opt/local/lib/*/stats.so
       0x1037b0000 -        0x1037cbfe7 +grid.so (0)
<D7803832-352A-3FE7-B6E6-4DA15ED767AE> /opt/local/lib/*/grid.so
       0x1037d2000 -        0x1037fbff7 +libRblas.dylib (0)
<A50EB94C-F8EF-CE81-A706-1578808F1BA1>
/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libRblas.dylib
       0x104a03000 -        0x104ccffff +libR.dylib (2.15.3)
<A5F068D3-7995-316C-83DE-FBF8D6D75330>
/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libR.dylib
       0x104e10000 -        0x104ec6fcf +libgfortran.2.dylib (3)
<ACF1816E-EA8A-4DB9-A893-A4EF0CEFFFBA>
/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib
       0x104f0b000 -        0x104f35fd9 +libreadline.5.2.dylib (5.2)
/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib
    0x7fff6a11b000 -     0x7fff6a14f93f  dyld (210.2.3)
<6900F2BA-DB48-3B78-B668-58FC0CF6BCB8> /usr/lib/dyld
    0x7fff8bdce000 -     0x7fff8bdd0ff7  libunc.dylib (25)
<92805328-CD36-34FF-9436-571AB0485072> /usr/lib/system/libunc.dylib
    0x7fff8c05a000 -     0x7fff8c07cff7  libxpc.dylib (140.42)
<BBE558BD-5E55-35E4-89ED-1AA6B056D05A> /usr/lib/system/libxpc.dylib
    0x7fff8c07d000 -     0x7fff8c08bfff  libcommonCrypto.dylib (60027)
<BAAFE0C9-BB86-3CA7-88C0-E3CBA98DA06F> /usr/lib/system/libcommonCrypto.dylib
    0x7fff8c18b000 -     0x7fff8c1c3fff  libncurses.5.4.dylib (37.3)
<68D5B5F5-8252-3F1E-AFF1-C6AFE145DBC1> /usr/lib/libncurses.5.4.dylib
    0x7fff8c5d6000 -     0x7fff8c625ff7  libcorecrypto.dylib (106.2)
<CE0C29A3-C420-339B-ADAA-52F4683233CC> /usr/lib/system/libcorecrypto.dylib
    0x7fff8c689000 -     0x7fff8c6a4ff7  libsystem_kernel.dylib
(2050.22.13) <5A961E2A-CFB8-362B-BC43-122704AEB047>
/usr/lib/system/libsystem_kernel.dylib
    0x7fff8c87d000 -     0x7fff8c883fff  libmacho.dylib (829)
<BF332AD9-E89F-387E-92A4-6E1AB74BD4D9> /usr/lib/system/libmacho.dylib
    0x7fff8c8b0000 -     0x7fff8c8deff7  libsystem_m.dylib (3022.6)
<B434BE5C-25AB-3EBD-BAA7-5304B34E3441> /usr/lib/system/libsystem_m.dylib
    0x7fff8cee9000 -     0x7fff8ceeefff  libcache.dylib (57)
<65187C6E-3FBF-3EB8-A1AA-389445E2984D> /usr/lib/system/libcache.dylib
    0x7fff8cfa9000 -     0x7fff8cfb1ff7  libsystem_dnssd.dylib (379.37)
<616FC901-151E-38BF-B2C4-24A351C5FAAD> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff8d8a7000 -     0x7fff8d8a7fff  libkeymgr.dylib (25)
<CC9E3394-BE16-397F-926B-E579B60EE429> /usr/lib/system/libkeymgr.dylib
    0x7fff8db63000 -     0x7fff8db64fff  libsystem_blocks.dylib (59)
<D92DCBC3-541C-37BD-AADE-ACC75A0C59C8>
/usr/lib/system/libsystem_blocks.dylib
    0x7fff8e33a000 -     0x7fff8e33dff7  libdyld.dylib (210.2.3)
<F59367C9-C110-382B-A695-9035A6DD387E> /usr/lib/system/libdyld.dylib
    0x7fff8e33e000 -     0x7fff8e374fff  libsystem_info.dylib (406.17)
<4FFCA242-7F04-365F-87A6-D4EFB89503C1> /usr/lib/system/libsystem_info.dylib
    0x7fff8f1dc000 -     0x7fff8f1f1ff7  libdispatch.dylib (228.23)
<D26996BF-FC57-39EB-8829-F63585561E09> /usr/lib/system/libdispatch.dylib
    0x7fff8f26b000 -     0x7fff8f26cff7  libremovefile.dylib (23.2)
<6763BC8E-18B8-3AD9-8FFA-B43713A7264F> /usr/lib/system/libremovefile.dylib
    0x7fff8f693000 -     0x7fff8f69bfff  liblaunch.dylib (442.26.2)
<2F71CAF8-6524-329E-AC56-C506658B4C0C> /usr/lib/system/liblaunch.dylib
    0x7fff8fdb0000 -     0x7fff8fdc2ff7  libz.1.dylib (43)
<2A1551E8-A272-3DE5-B692-955974FE1416> /usr/lib/libz.1.dylib
    0x7fff90d1a000 -     0x7fff90f04ff7  com.apple.CoreFoundation (6.8 -
744.18) <A60C3C9B-3764-3291-844C-C487ACF77C2C>
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
    0x7fff913b8000 -     0x7fff913bffff  libcopyfile.dylib (89)
<876573D0-E907-3566-A108-577EAD1B6182> /usr/lib/system/libcopyfile.dylib
    0x7fff9284a000 -     0x7fff92850ff7  libunwind.dylib (35.1)
<21703D36-2DAB-3D8B-8442-EAAB23C060D3> /usr/lib/system/libunwind.dylib
    0x7fff934c2000 -     0x7fff934c3fff  libDiagnosticMessagesClient.dylib
(8) <8548E0DC-0D2F-30B6-B045-FE8A038E76D8>
/usr/lib/libDiagnosticMessagesClient.dylib
    0x7fff937d9000 -     0x7fff937daff7  libsystem_sandbox.dylib (220.2)
<6838A6FD-8626-3356-BB4F-BB4787216207>
/usr/lib/system/libsystem_sandbox.dylib
    0x7fff937db000 -     0x7fff938d0fff  libiconv.2.dylib (34)
<FEE8B996-EB44-37FA-B96E-D379664DEFE1> /usr/lib/libiconv.2.dylib
    0x7fff953b3000 -     0x7fff954cb92f  libobjc.A.dylib (532.2)
<90D31928-F48D-3E37-874F-220A51FD9E37> /usr/lib/libobjc.A.dylib
    0x7fff958a8000 -     0x7fff95910ff7  libc++.1.dylib (65.1)
<20E31B90-19B9-3C2A-A9EB-474E08F9FE05> /usr/lib/libc++.1.dylib
    0x7fff95d39000 -     0x7fff95d5eff7  libc++abi.dylib (26)
<D86169F3-9F31-377A-9AF3-DB17142052E4> /usr/lib/libc++abi.dylib
    0x7fff95dc2000 -     0x7fff95dcdfff  libsystem_notify.dylib (98.5)
<C49275CC-835A-3207-AFBA-8C01374927B6>
/usr/lib/system/libsystem_notify.dylib
    0x7fff95dd1000 -     0x7fff95e3afff  libstdc++.6.dylib (56)
<EAA2B53E-EADE-39CF-A0EF-FB9D4940672A> /usr/lib/libstdc++.6.dylib
    0x7fff95f1e000 -     0x7fff95f20fff  libquarantine.dylib (52)
<4BE2E642-A14F-340A-B482-5BD2AEFD9C24> /usr/lib/system/libquarantine.dylib
    0x7fff95f21000 -     0x7fff95f6dff7  libauto.dylib (185.1)
<73CDC482-16E3-3FC7-9BB4-FBA2DA44DBC2> /usr/lib/libauto.dylib
    0x7fff96355000 -     0x7fff9635afff  libcompiler_rt.dylib (30)
<08F8731D-5961-39F1-AD00-4590321D24A9> /usr/lib/system/libcompiler_rt.dylib
    0x7fff963c4000 -     0x7fff965c4fff  libicucore.A.dylib (491.11.2)
<FD6282D8-DF3F-3842-8C2E-CF478D2B9669> /usr/lib/libicucore.A.dylib
    0x7fff973c2000 -     0x7fff9748eff7  libsystem_c.dylib (825.26)
<4C9EB006-FE1F-3F8F-8074-DFD94CF2CE7B> /usr/lib/system/libsystem_c.dylib
    0x7fff974b4000 -     0x7fff974b5ff7  libdnsinfo.dylib (453.19)
<14202FFB-C3CA-3FCC-94B0-14611BF8692D> /usr/lib/system/libdnsinfo.dylib
    0x7fff98479000 -     0x7fff9847aff7  libSystem.B.dylib (169.3)
<FF25248A-574C-32DB-952F-B948C389B2A4> /usr/lib/libSystem.B.dylib
    0x7fff985d4000 -     0x7fff985e2ff7  libsystem_network.dylib (77.10)
<0D99F24E-56FE-380F-B81B-4A4C630EE587>
/usr/lib/system/libsystem_network.dylib

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]]

