[BUGZILLA #15665] Applying function on phyla tree created by bionjs causes fatal R crash

Created attachment 1562 [details] tree that causes crash

A tree created using bionjs causes fatal R crash when other functions (eg. plot, bullseye or multi2di). I have attached a RData file of the tree and the crash report.

Bug report:

Process: rsession [80104] Path: /Applications/RStudio.app/Contents/MacOS/rsession Identifier: rsession Version: ??? Code Type: X86-64 (Native) Parent Process: RStudio [71770] Responsible: RStudio [71770] User ID: 502

Date/Time: 2014-02-13 12:43:26.736 -0500 OS Version: Mac OS X 10.9.1 (13B42) Report Version: 11 Anonymous UUID: 03E0EEA6-5AFC-19C8-280B-A7B4754E4394

Sleep/Wake UUID: 202F11A9-CF23-479E-8DBE-2AC7A15D3F43

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x00007fa33aed6ed4

VM Regions Near 0x7fa33aed6ed4: MALLOC_LARGE 0000000107929000-0000000107bfd000 [ 2896K] rw-/rwx SM=PRV
--> MALLOC_TINY 00007fa433c00000-00007fa434000000 [ 4096K] rw-/rwx SM=COW

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 ape.so 0x0000000102029e69 neworder_phylo + 169 (reorder_phylo.c:68) 1 libR.dylib 0x00000001013d3efa do_dotCode + 4874 (dotcode.c:1736) 2 libR.dylib 0x00000001014062ad Rf_eval + 1181 (eval.c:642) 3 libR.dylib 0x00000001014116b6 Rf_DispatchOrEval + 214 (eval.c:2455) 4 libR.dylib 0x0000000101497691 do_subset2 + 65 (subset.c:841) 5 libR.dylib 0x000000010140611f Rf_eval + 783 (eval.c:614) 6 libR.dylib 0x0000000101412717 do_set + 343 (eval.c:1902) 7 libR.dylib 0x000000010140611f Rf_eval + 783 (eval.c:614) 8 libR.dylib 0x0000000101412a70 do_begin + 384 (eval.c:1573) 9 libR.dylib 0x000000010140611f Rf_eval + 783 (eval.c:614) 10 libR.dylib 0x000000010140611f Rf_eval + 783 (eval.c:614) 11 libR.dylib 0x0000000101412a70 do_begin + 384 (eval.c:1573) 12 libR.dylib 0x000000010140611f Rf_eval + 783 (eval.c:614) 13 libR.dylib 0x000000010141035e Rf_applyClosure + 1422 (eval.c:1019) 14 libR.dylib 0x000000010144375f Rf_usemethod + 1343 (objects.c:347) 15 libR.dylib 0x0000000101443ed6 do_usemethod + 774 (objects.c:449) 16 libR.dylib 0x0000000101408a93 bcEval + 9683 (eval.c:4647) 17 libR.dylib 0x0000000101405f06 Rf_eval + 246 (eval.c:545) 18 libR.dylib 0x000000010141035e Rf_applyClosure + 1422 (eval.c:1019) 19 libR.dylib 0x000000010140634e Rf_eval + 1342 (eval.c:661) 20 libR.dylib 0x0000000101412717 do_set + 343 (eval.c:1902) 21 libR.dylib 0x000000010140611f Rf_eval + 783 (eval.c:614) 22 libR.dylib 0x0000000101412a70 do_begin + 384 (eval.c:1573) 23 libR.dylib 0x000000010140611f Rf_eval + 783 (eval.c:614) 24 libR.dylib 0x000000010141035e Rf_applyClosure + 1422 (eval.c:1019) 25 libR.dylib 0x000000010144375f Rf_usemethod + 1343 (objects.c:347) 26 libR.dylib 0x0000000101443ed6 do_usemethod + 774 (objects.c:449) 27 libR.dylib 0x0000000101408a93 bcEval + 9683 (eval.c:4647) 28 libR.dylib 0x0000000101405f06 Rf_eval + 246 (eval.c:545) 29 libR.dylib 0x000000010141035e Rf_applyClosure + 1422 (eval.c:1019) 30 libR.dylib 0x000000010140634e Rf_eval + 1342 (eval.c:661) 31 libR.dylib 0x0000000101433fcf Rf_ReplIteration + 879 (main.c:258) 32 libR.dylib 0x0000000101434643 run_Rmainloop + 195 (main.c:307) 33 rsession 0x0000000100b1a02b r::session::runEmbeddedR(core::FilePath const&, core::FilePath const&, bool, bool, SA_TYPE, r::session::Callbacks const&, r::session::InternalCallbacks*) + 427 34 rsession 0x0000000100afcefa r::session::run(r::session::ROptions const&, r::session::RCallbacks const&) + 2474 35 rsession 0x00000001006bbfd8 main + 15640 36 rsession 0x0000000100697d14 start + 52

Thread 1: 0 libsystem_kernel.dylib 0x00007fff8aae2716 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff88820c3b _pthread_cond_wait + 727 2 rsession 0x000000010069db4d bool boost::condition_variable_any::do_timed_wait<boost::unique_lock >(boost::unique_lock&, timespec const&) + 77 3 rsession 0x0000000100a75030 core::thread::ThreadsafeQueue<core::system::file_monitor::(anonymous namespace)::RegistrationCommand>::wait(boost::posix_time::time_duration const&) + 656 4 rsession 0x0000000100a751a7 core::system::file_monitor::(anonymous namespace)::checkForInput() + 215 5 rsession 0x0000000100a9ebd6 core::system::file_monitor::detail::run(boost::function<void ()> const&) + 70 6 rsession 0x0000000100a71c4d core::system::file_monitor::(anonymous namespace)::fileMonitorThreadMain() + 189 7 rsession 0x000000010095b50b boost::detail::thread_data<boost::function<void ()> >::run() + 75 8 rsession 0x0000000100b80481 thread_proxy + 161 9 libsystem_pthread.dylib 0x00007fff8881e899 _pthread_body + 138 10 libsystem_pthread.dylib 0x00007fff8881e72a _pthread_start + 137 11 libsystem_pthread.dylib 0x00007fff88822fc9 thread_start + 13

Thread 2: 0 libsystem_kernel.dylib 0x00007fff8aae2716 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff88820c3b _pthread_cond_wait + 727 2 rsession 0x0000000100b829d9 boost::condition_variable::do_timed_wait(boost::unique_lock&, timespec const&) + 217 3 rsession 0x0000000100b811d8 boost::this_thread::sleep(boost::posix_time::ptime const&) + 216 4 rsession 0x00000001006bd00a (anonymous namespace)::detectParentTermination() + 122 5 rsession 0x000000010095b50b boost::detail::thread_data<boost::function<void ()> >::run() + 75 6 rsession 0x0000000100b80481 thread_proxy + 161 7 libsystem_pthread.dylib 0x00007fff8881e899 _pthread_body + 138 8 libsystem_pthread.dylib 0x00007fff8881e72a _pthread_start + 137 9 libsystem_pthread.dylib 0x00007fff88822fc9 thread_start + 13

Thread 3: 0 libsystem_kernel.dylib 0x00007fff8aae29aa __select + 10 1 rsession 0x0000000100802039 boost::asio::detail::select_reactor::run(bool, boost::asio::detail::op_queue&) + 1161 2 rsession 0x000000010080189d boost::asio::detail::task_io_service::do_run_one(boost::asio::detail::scoped_lock&, boost::asio::detail::task_io_service::thread_info&, boost::asio::detail::op_queue&, boost::system::error_code const&) + 333 3 rsession 0x00000001008014cd boost::asio::detail::task_io_service::run(boost::system::error_code&) + 285 4 rsession 0x000000010092a059 boost::asio::io_service::run() + 41 5 rsession 0x0000000100b80481 thread_proxy + 161 6 libsystem_pthread.dylib 0x00007fff8881e899 _pthread_body + 138 7 libsystem_pthread.dylib 0x00007fff8881e72a _pthread_start + 137 8 libsystem_pthread.dylib 0x00007fff88822fc9 thread_start + 13

Thread 4: 0 libsystem_kernel.dylib 0x00007fff8aae2716 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff88820c3b _pthread_cond_wait + 727 2 rsession 0x000000010069db4d bool boost::condition_variable_any::do_timed_wait<boost::unique_lock >(boost::unique_lock&, timespec const&) + 77 3 rsession 0x000000010069ccdf session::ClientEventQueue::waitForEvent(boost::posix_time::time_duration const&) + 367 4 rsession 0x00000001006a5aaf session::ClientEventService::run() + 1615 5 rsession 0x0000000100b80481 thread_proxy + 161 6 libsystem_pthread.dylib 0x00007fff8881e899 _pthread_body + 138 7 libsystem_pthread.dylib 0x00007fff8881e72a _pthread_start + 137 8 libsystem_pthread.dylib 0x00007fff88822fc9 thread_start + 13

Thread 5:: Dispatch queue: com.apple.libdispatch-manager 0 libsystem_kernel.dylib 0x00007fff8aae3662 kevent64 + 10 1 libdispatch.dylib 0x00007fff8af4443d _dispatch_mgr_invoke + 239 2 libdispatch.dylib 0x00007fff8af44152 _dispatch_mgr_thread + 52

Thread 6: 0 libsystem_kernel.dylib 0x00007fff8aae29aa __select + 10 1 rsession 0x0000000100a8bae6 core::system::(anonymous namespace)::standardStreamCaptureThread(int, boost::function<void (std::string const&)> const&, int, boost::function<void (std::string const&)> const&) + 294 2 rsession 0x0000000100b80481 thread_proxy + 161 3 libsystem_pthread.dylib 0x00007fff8881e899 _pthread_body + 138 4 libsystem_pthread.dylib 0x00007fff8881e72a _pthread_start + 137 5 libsystem_pthread.dylib 0x00007fff88822fc9 thread_start + 13

Thread 0 crashed with X86 Thread State (64-bit): rax: 0xffffffffc000002b rbx: 0x00007fa43b01d6c0 rcx: 0x0000000000000009 rdx: 0x000000000000002b rdi: 0x00000000c0000000 rsi: 0x00000000c0000001 rbp: 0x00007fff5f564670 rsp: 0x00007fff5f564610 r8: 0x000000000000000b r9: 0x00007fa433e00000 r10: 0x0000000063b00330 r11: 0x0000000064e25200 r12: 0x00007fa43aed6e28 r13: 0x00007fa433e84d58 r14: 0x00007fa43b01e4c0 r15: 0x0000000000000025 rip: 0x0000000102029e69 rfl: 0x0000000000010283 cr2: 0x00007fa33aed6ed4

Logical CPU: 1 Error Code: 0x00000006 Trap Number: 14

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600.4) <36B2B009-C35E-3F21-824E-E0D00E7808C7> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices 0x7fff93abb000 - 0x7fff93ba5fff libsqlite3.dylib (158) <00269BF9-43BE-39E0-9C85-24585B9923C8> /usr/lib/libsqlite3.dylib 0x7fff93ba6000 - 0x7fff93cabfff com.apple.ImageIO.framework (3.3.0 - 1038) <2C058216-C6D8-3380-A7EA-92A3F04520C1> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO 0x7fff93cc1000 - 0x7fff93d03ff7 libauto.dylib (185.5) /usr/lib/libauto.dylib 0x7fff93d04000 - 0x7fff93d0cffc libGFXShared.dylib (9.0.83) <11A621C3-37A0-39CE-A69B-8739021BD79D> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib 0x7fff93e51000 - 0x7fff93e63ff7 com.apple.MultitouchSupport.framework (245.13 - 245.13) /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport 0x7fff94440000 - 0x7fff94458ff7 com.apple.GenerationalStorage (2.0 - 160.2) <79629AC7-896F-3302-8AC1-4939020F08C3> /System/Library/PrivateFrameworks/GenerationalStorage.framework/Versions/A/GenerationalStorage 0x7fff947c3000 - 0x7fff947c8fff com.apple.DiskArbitration (2.6 - 2.6) /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration 0x7fff94900000 - 0x7fff9490afff libcommonCrypto.dylib (60049) <8C4F0CA0-389C-3EDC-B155-E62DD2187E1D> /usr/lib/system/libcommonCrypto.dylib 0x7fff9490b000 - 0x7fff9490bfff com.apple.Accelerate (1.9 - Accelerate 1.9) <509BB27A-AE62-366D-86D8-0B06D217CF56> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate 0x7fff94952000 - 0x7fff94a36fff com.apple.coreui (2.1 - 231) <432DB40C-6B7E-39C8-9FB5-B95917930056> /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI 0x7fff94a37000 - 0x7fff94a40ff3 libsystem_notify.dylib (121) <52571EC3-6894-37E4-946E-064B021ED44E> /usr/lib/system/libsystem_notify.dylib 0x7fff94a41000 - 0x7fff94aa4ff7 com.apple.SystemConfiguration (1.13 - 1.13) /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration 0x7fff94aa8000 - 0x7fff94aa9ff7 libsystem_sandbox.dylib (278.10) /usr/lib/system/libsystem_sandbox.dylib 0x7fff94da4000 - 0x7fff94da5fff liblangid.dylib (117) <9546E641-F730-3AB0-B3CD-E0E2FDD173D9> /usr/lib/liblangid.dylib 0x7fff94da6000 - 0x7fff94dd6fff libncurses.5.4.dylib (42) /usr/lib/libncurses.5.4.dylib 0x7fff94dec000 - 0x7fff94dedff7 libsystem_blocks.dylib (63) /usr/lib/system/libsystem_blocks.dylib 0x7fff94def000 - 0x7fff94df2fff libCoreVMClient.dylib (58.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib 0x7fff94dff000 - 0x7fff94e4dff9 libstdc++.6.dylib (60) <0241E6A4-1368-33BE-950B-D0A175C41F54> /usr/lib/libstdc++.6.dylib 0x7fff94f91000 - 0x7fff94fc0ff5 com.apple.GSS (4.0 - 2.0) /System/Library/Frameworks/GSS.framework/Versions/A/GSS 0x7fff94ff3000 - 0x7fff950b6ff7 com.apple.backup.framework (1.5.1 - 1.5.1) /System/Library/PrivateFrameworks/Backup.framework/Versions/A/Backup

External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 1 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: 197977 thread_create: 1898 thread_set_state: 27

VM Region Summary: ReadOnly portion of Libraries: Total=180.5M resident=96.9M(54%) swapped_out_or_unallocated=83.6M(46%) Writable regions: Total=209.2M written=129.8M(62%) resident=139.3M(67%) swapped_out=0K(0%) unallocated=69.9M(33%)

REGION TYPE VIRTUAL =========== ======= Dispatch continuations 4096K Kernel Alloc Once 4K MALLOC 154.3M MALLOC (admin) 32K STACK GUARD 56.0M Stack 10.6M VM_ALLOCATE 24K DATA 59.3M IMAGE 528K LINKEDIT 74.4M TEXT 106.1M __UNICODE 544K mapped file 22.5M shared memory 4K =========== ======= TOTAL 488.2M

METADATA

Bug author - Etienne Low-Decarie
Creation time - 2014-02-13 19:10:53 UTC
Bugzilla link
Status - CLOSED CONTRIBUTED PACKAGE
Alias - None
Component - Add-ons
Version - R 3.0.2
Hardware - x86_64/x64/amd64 (64-bit) OS X Mavericks
Importance - P5 enhancement
Assignee - R-core
URL -
Modification time - 2014-02-13 19:24 UTC

MichaelChirico / r-bugs

[BUGZILLA #15665] Applying function on phyla tree created by bionjs causes fatal R crash #5221

METADATA

METADATA