[R-SIG-Mac] Rpy2 and Mac OS X 10.8.3
Simon Urbanek
simon.urbanek at r-project.org
Tue Apr 2 16:26:05 CEST 2013
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
>
> 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]]
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
More information about the R-SIG-Mac
mailing list