MatLab Error Messages

Hi All,

I’m sure this is a very rookie mistake, but I’m just trying to get acquainted with CP and MatLab and am running it on a Mac. I have installed CP 5811 and MatLab 7.4 and my computer already has X11, so that’s not the problem. I find that I can open MatLab, and then through MatLab open CP, and it opens properly, and iI cal load a preexisting pipeline into the program just fine, but when I try to modify the program at all, or when I open preferences and try to change the automatic input / output folders, the whole system shuts down, and I get the following MatLab error, the gist of which seems to be that Thread 2 crashed. Does this mean anything to anyone? I’m fairly sure I have something set up wrong, but I can’t figure out where:

MATLAB quit unexpectedly
Problem Details and System Configuration:

Process: MATLAB [8155]
Path: /Applications/MATLAB74/bin/maci/MATLAB.app/Contents/MacOS/MATLAB
Identifier: com.mathworks.matlab
Version: MATLAB version 7.1 (2.1)
Code Type: X86 (Native)
Parent Process: ??? [1]

Date/Time: 2010-05-10 13:46:00.654 -0400
OS Version: Mac OS X 10.6.2 (10C540)
Report Version: 6

Interval Since Last Report: 122416 sec
Crashes Since Last Report: 1
Per-App Interval Since Last Report: 288 sec
Per-App Crashes Since Last Report: 1
Anonymous UUID: 797C853B-B501-4978-B5C9-AE8541780AB9

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Crashed Thread: 2

Application Specific Information:
abort() called

Thread 0: Dispatch queue: com.apple.main-thread
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 com.apple.CoreFoundation 0x9075777f __CFRunLoopRun + 2079
3 com.apple.CoreFoundation 0x90756864 CFRunLoopRunSpecific + 452
4 com.apple.CoreFoundation 0x90756691 CFRunLoopRunInMode + 97
5 com.apple.HIToolbox 0x969cbf0c RunCurrentEventLoopInMode + 392
6 com.apple.HIToolbox 0x969cbcc3 ReceiveNextEventCommon + 354
7 com.apple.HIToolbox 0x96b53c02 _AcquireNextEvent + 54
8 com.apple.HIToolbox 0x96b49944 RunApplicationEventLoop + 228
9 libmwmcr.dylib 0x002defee mcr_kickoff_cfrunloop(void* ()(void), void*, bool) + 262
10 libmwmcr.dylib 0x002df166 mcr_run_main(int (*)(int, char**), int, char**) + 244
11 com.mathworks.matlab 0x00002794 start + 1948
12 com.mathworks.matlab 0x000020fa start + 258
13 com.mathworks.matlab 0x00002021 start + 41

Thread 1: Dispatch queue: com.apple.libdispatch-manager
0 libSystem.B.dylib 0x94c390ea kevent + 10
1 libSystem.B.dylib 0x94c39804 _dispatch_mgr_invoke + 215
2 libSystem.B.dylib 0x94c38cc3 _dispatch_queue_invoke + 163
3 libSystem.B.dylib 0x94c38a68 _dispatch_worker_thread2 + 234
4 libSystem.B.dylib 0x94c384f1 _pthread_wqthread + 390
5 libSystem.B.dylib 0x94c38336 start_wqthread + 30

Thread 2 Crashed:
0 libSystem.B.dylib 0x94c7fa4e __semwait_signal_nocancel + 10
1 libSystem.B.dylib 0x94c7f932 nanosleep$NOCANCEL$UNIX2003 + 166
2 libSystem.B.dylib 0x94cfb39a usleep$NOCANCEL$UNIX2003 + 61
3 libSystem.B.dylib 0x94d1ca50 abort + 105
4 libstdc++.6.dylib 0x967a5fda __gnu_cxx::__verbose_terminate_handler() + 433
5 libstdc++.6.dylib 0x967a417a __cxxabiv1::__terminate(void ()()) + 10
6 libstdc++.6.dylib 0x967a41ba __cxxabiv1::__unexpected(void (
)()) + 0
7 libstdc++.6.dylib 0x967a42b8 __gxx_exception_cleanup(_Unwind_Reason_Code, _Unwind_Exception*) + 0
8 libut.dylib 0x00028005 utThrowCPPException + 97
9 libmx.dylib 0x000f05cb mxSetLastErrIdAndMsg + 75
10 libmx.dylib 0x000f0174 mxErrorDisplay + 356
11 libmx.dylib 0x000f0208 mxErrMsgIdAndTxt + 42
12 libmx.dylib 0x00116a8c void std::reverse<mxArray_tag**>(mxArray_tag**, mxArray_tag**) + 1190
13 libmx.dylib 0x00116cf9 void std::reverse<mxArray_tag**>(mxArray_tag**, mxArray_tag**) + 1811
14 libmwm_interpreter.dylib 0x003ed30b inConvertToLHSType + 180509
15 libmwm_interpreter.dylib 0x003ed3c2 inConvertToLHSType + 180692
16 ??? 0x2a98e9d7 0 + 714664407
17 libmwm_interpreter.dylib 0x003c4359 inConvertToLHSType + 12651
18 libmwm_interpreter.dylib 0x003d2adc inConvertToLHSType + 71918
19 libmwm_interpreter.dylib 0x003d2c9f inConvertToLHSType + 72369
20 libmwm_interpreter.dylib 0x003d2d28 inConvertToLHSType + 72506
21 libmwm_interpreter.dylib 0x003a777d inSetAccelFeatureEnabled + 12297
22 libmwm_interpreter.dylib 0x0038e0ff inRegisterLineNoHook + 9227
23 libmwm_interpreter.dylib 0x0047e2cc mdSetContextProtected::mdSetContextProtected(bool) + 892
24 libmwm_interpreter.dylib 0x003901d2 inRegisterLineNoHook + 17630
25 libmwm_interpreter.dylib 0x003906f7 inRegisterLineNoHook + 18947
26 libmwm_interpreter.dylib 0x003c2bd8 inConvertToLHSType + 6634
27 libmwm_interpreter.dylib 0x0039a228 inTriggerDebugEvent + 1922
28 libmwm_dispatcher.dylib 0x003301b2 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) + 188
29 libmwm_interpreter.dylib 0x0047af27 Mdispatcher::lookup_binding(int, int, Mtypeidx_attributes**) + 235
30 libmwm_interpreter.dylib 0x00412b49 inConvertToLHSType + 334171
31 libmwm_interpreter.dylib 0x00414b94 inConvertToLHSType + 342438
32 libmwm_interpreter.dylib 0x004151fe inConvertToLHSType + 344080
33 libmwm_interpreter.dylib 0x003c41a0 inConvertToLHSType + 12210
34 libmwm_interpreter.dylib 0x003d2c48 inConvertToLHSType + 72282
35 libmwm_interpreter.dylib 0x003d2d28 inConvertToLHSType + 72506
36 libmwm_interpreter.dylib 0x003a777d inSetAccelFeatureEnabled + 12297
37 libmwm_interpreter.dylib 0x0038e0ff inRegisterLineNoHook + 9227
38 libmwm_interpreter.dylib 0x0047e2cc mdSetContextProtected::mdSetContextProtected(bool) + 892
39 libmwm_interpreter.dylib 0x003901d2 inRegisterLineNoHook + 17630
40 libmwm_interpreter.dylib 0x003906f7 inRegisterLineNoHook + 18947
41 libmwm_interpreter.dylib 0x003c2bd8 inConvertToLHSType + 6634
42 libmwm_interpreter.dylib 0x0039a228 inTriggerDebugEvent + 1922
43 libmwm_dispatcher.dylib 0x003301b2 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) + 188
44 libmwm_interpreter.dylib 0x003b558a inRunSaveObjFunction + 7210
45 libmwm_interpreter.dylib 0x003b5c74 inRunSaveObjFunction + 8980
46 libmwm_interpreter.dylib 0x0038d984 inRegisterLineNoHook + 7312
47 libmwm_interpreter.dylib 0x0038f5c3 inRegisterLineNoHook + 14543
48 libmwm_interpreter.dylib 0x0047e2cc mdSetContextProtected::mdSetContextProtected(bool) + 892
49 libmwm_interpreter.dylib 0x003901d2 inRegisterLineNoHook + 17630
50 libmwm_interpreter.dylib 0x0039040f inRegisterLineNoHook + 18203
51 libmwm_interpreter.dylib 0x0038a50f inAnonymousFunction + 6167
52 libmwm_interpreter.dylib 0x0038ac30 inEvalExpWithIsVarFcn + 208
53 libmwm_interpreter.dylib 0x00387f1b inEvalExpInWS + 137
54 libmwgui.dylib 0x047c28e8 MCallback::_execute(mxArray_tag*, mxArray_tag*, int, mxArray_tag**) const + 204
55 libmwgui.dylib 0x047c3752 MCallback::execute(mxArray_tag*, mxArray_tag*) const + 442
56 libmwgui.dylib 0x047c37e1 ExecuteMCallback(MCallback const*, mxArray_tag*, mxArray_tag*) + 31
57 libmwhg.dylib 0x0495cc07 GO_OkToRender(GObject_tag*, bool) + 4501
58 libmwhg.dylib 0x0495cfd8 goCallInternalCallback + 324
59 libmwhg.dylib 0x0493921b UpdateFactoryControlColor + 6287
60 libmwhg.dylib 0x048fbc91 hgImage + 16191
61 libmwhg.dylib 0x048f99f7 hgImage + 7333
62 libmwudd.dylib 0x0471dedd uddSetListenerRecursionWarning(bool) + 401
63 libmwudd.dylib 0x0471e5db UDListenerManagerHost::notifyEvent(UDDatabaseClient*, UDEventSource const*, UDEventInfo const*, UDEvent*) + 73
64 libmwudd.dylib 0x04718190 UDEventInfo::send(UDDatabaseClient*, UDInterface*, UDEvent*) + 92
65 libmwudd_mi.dylib 0x04ab8234 0x4ab6000 + 8756
66 libmwuix.dylib 0x04b4dab5 UIX_OverrideNavigationTranslations + 683
67 libmwuix.dylib 0x04b580f5 UIX_AssertXThread_internal + 727
68 libmwuix.dylib 0x04b52fa2 ws_ProcessOneEventBlocking() + 110
69 libmwhg.dylib 0x0495bfdc GO_OkToRender(GObject_tag*, bool) + 1386
70 libmwm_dispatcher.dylib 0x0033926f mdMxarrayFunctionHandle::freeze() + 2113
71 libmwm_dispatcher.dylib 0x0031d39f Mfh_MATLAB_fn::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) + 123
72 libmwm_interpreter.dylib 0x003b558a inRunSaveObjFunction + 7210
73 libmwm_interpreter.dylib 0x003b5c74 inRunSaveObjFunction + 8980
74 libmwm_interpreter.dylib 0x0038d984 inRegisterLineNoHook + 7312
75 libmwm_interpreter.dylib 0x0038f5c3 inRegisterLineNoHook + 14543
76 libmwm_interpreter.dylib 0x0047e2cc mdSetContextProtected::mdSetContextProtected(bool) + 892
77 libmwm_interpreter.dylib 0x003901d2 inRegisterLineNoHook + 17630
78 libmwm_interpreter.dylib 0x003906f7 inRegisterLineNoHook + 18947
79 libmwm_interpreter.dylib 0x003c2bd8 inConvertToLHSType + 6634
80 libmwm_interpreter.dylib 0x0039a228 inTriggerDebugEvent + 1922
81 libmwm_dispatcher.dylib 0x003301b2 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) + 188
82 libmwm_interpreter.dylib 0x0047af27 Mdispatcher::lookup_binding(int, int, Mtypeidx_attributes**) + 235
83 libmwm_interpreter.dylib 0x00412b49 inConvertToLHSType + 334171
84 libmwm_interpreter.dylib 0x00414b94 inConvertToLHSType + 342438
85 libmwm_interpreter.dylib 0x004151fe inConvertToLHSType + 344080
86 libmwm_interpreter.dylib 0x003c41a0 inConvertToLHSType + 12210
87 libmwm_interpreter.dylib 0x003d2c48 inConvertToLHSType + 72282
88 libmwm_interpreter.dylib 0x003d2d28 inConvertToLHSType + 72506
89 libmwm_interpreter.dylib 0x003a777d inSetAccelFeatureEnabled + 12297
90 libmwm_interpreter.dylib 0x0038e0ff inRegisterLineNoHook + 9227
91 libmwm_interpreter.dylib 0x0047e2cc mdSetContextProtected::mdSetContextProtected(bool) + 892
92 libmwm_interpreter.dylib 0x003901d2 inRegisterLineNoHook + 17630
93 libmwm_interpreter.dylib 0x003906f7 inRegisterLineNoHook + 18947
94 libmwm_interpreter.dylib 0x003c2bd8 inConvertToLHSType + 6634
95 libmwm_interpreter.dylib 0x0039a228 inTriggerDebugEvent + 1922
96 libmwm_dispatcher.dylib 0x003301b2 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) + 188
97 libmx.dylib 0x000f27c7 mxFevalFunctionHandle + 53
98 libmwm_dispatcher.dylib 0x0033926f mdMxarrayFunctionHandle::freeze() + 2113
99 libmwm_dispatcher.dylib 0x0031d39f Mfh_MATLAB_fn::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) + 123
100 libmwm_interpreter.dylib 0x003b558a inRunSaveObjFunction + 7210
101 libmwm_interpreter.dylib 0x003b5c74 inRunSaveObjFunction + 8980
102 libmwm_interpreter.dylib 0x0038d984 inRegisterLineNoHook + 7312
103 libmwm_interpreter.dylib 0x0038f5c3 inRegisterLineNoHook + 14543
104 libmwm_interpreter.dylib 0x0047e2cc mdSetContextProtected::mdSetContextProtected(bool) + 892
105 libmwm_interpreter.dylib 0x003901d2 inRegisterLineNoHook + 17630
106 libmwm_interpreter.dylib 0x003906f7 inRegisterLineNoHook + 18947
107 libmwm_interpreter.dylib 0x003c2bd8 inConvertToLHSType + 6634
108 libmwm_interpreter.dylib 0x0039a228 inTriggerDebugEvent + 1922
109 libmwm_dispatcher.dylib 0x003301b2 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) + 188
110 libmwm_interpreter.dylib 0x003b558a inRunSaveObjFunction + 7210
111 libmwm_interpreter.dylib 0x003b5c74 inRunSaveObjFunction + 8980
112 libmwm_interpreter.dylib 0x0038d984 inRegisterLineNoHook + 7312
113 libmwm_interpreter.dylib 0x0038f5c3 inRegisterLineNoHook + 14543
114 libmwm_interpreter.dylib 0x0047e2cc mdSetContextProtected::mdSetContextProtected(bool) + 892
115 libmwm_interpreter.dylib 0x003901d2 inRegisterLineNoHook + 17630
116 libmwm_interpreter.dylib 0x003906f7 inRegisterLineNoHook + 18947
117 libmwm_interpreter.dylib 0x003c2bd8 inConvertToLHSType + 6634
118 libmwm_interpreter.dylib 0x0039a228 inTriggerDebugEvent + 1922
119 libmwm_dispatcher.dylib 0x003301b2 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) + 188
120 libmwm_interpreter.dylib 0x003b558a inRunSaveObjFunction + 7210
121 libmwm_interpreter.dylib 0x003b5c74 inRunSaveObjFunction + 8980
122 libmwm_interpreter.dylib 0x0038d984 inRegisterLineNoHook + 7312
123 libmwm_interpreter.dylib 0x0038f5c3 inRegisterLineNoHook + 14543
124 libmwm_interpreter.dylib 0x0047e2cc mdSetContextProtected::mdSetContextProtected(bool) + 892
125 libmwm_interpreter.dylib 0x003901d2 inRegisterLineNoHook + 17630
126 libmwm_interpreter.dylib 0x0039040f inRegisterLineNoHook + 18203
127 libmwm_interpreter.dylib 0x0038a50f inAnonymousFunction + 6167
128 libmwm_interpreter.dylib 0x0038ac30 inEvalExpWithIsVarFcn + 208
129 libmwm_interpreter.dylib 0x00387f1b inEvalExpInWS + 137
130 libmwgui.dylib 0x047c28e8 MCallback::_execute(mxArray_tag*, mxArray_tag*, int, mxArray_tag**) const + 204
131 libmwgui.dylib 0x047c3752 MCallback::execute(mxArray_tag*, mxArray_tag*) const + 442
132 libmwgui.dylib 0x047c37e1 ExecuteMCallback(MCallback const*, mxArray_tag*, mxArray_tag*) + 31
133 libmwhg.dylib 0x0495cc07 GO_OkToRender(GObject_tag*, bool) + 4501
134 libmwhg.dylib 0x0495cfd8 goCallInternalCallback + 324
135 libmwhg.dylib 0x0493dd6e goMenuActivated + 176
136 libmwhg.dylib 0x048f99f7 hgImage + 7333
137 libmwudd.dylib 0x0471dedd uddSetListenerRecursionWarning(bool) + 401
138 libmwudd.dylib 0x0471e5db UDListenerManagerHost::notifyEvent(UDDatabaseClient*, UDEventSource const*, UDEventInfo const*, UDEvent*) + 73
139 libmwudd.dylib 0x04718190 UDEventInfo::send(UDDatabaseClient*, UDInterface*, UDEvent*) + 92
140 libmwudd_mi.dylib 0x04ab8234 0x4ab6000 + 8756
141 libmwuix.dylib 0x04b4dab5 UIX_OverrideNavigationTranslations + 683
142 libmwuix.dylib 0x04b580f5 UIX_AssertXThread_internal + 727
143 libmwuix.dylib 0x04b5829d UIX_AssertXThread_internal + 1151
144 libmwbridge.dylib 0x002c20d0 ioCmdLineEditSave + 3618
145 libmwbridge.dylib 0x002c2209 ioCmdLineEditSave + 3931
146 libmwbridge.dylib 0x002c39c9 mnSetOEMCallbackActive(bool) + 199
147 libmwbridge.dylib 0x002c3b08 mnSetOEMCallbackActive(bool) + 518
148 libmwbridge.dylib 0x002c4156 mnParser + 418
149 libmwmcr.dylib 0x002e0a99 mcrInstance::mnParser() + 39
150 com.mathworks.matlab 0x00002907 start + 2319
151 libmwmcr.dylib 0x002df045 mcr_kickoff_cfrunloop(void* ()(void), void*, bool) + 349
152 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
153 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 3: Java: Exception Handler Thread
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libSystem.B.dylib 0x94c7e5d8 mach_msg_server + 520
3 libjvm.dylib 0x1a70ae25 JNI_CreateJavaVM_Impl + 61045
4 libjvm.dylib 0x1a70adca JNI_CreateJavaVM_Impl + 60954
5 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
6 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
7 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 4: Java: Gang worker#0 (Parallel GC Threads)
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a709f23 JNI_CreateJavaVM_Impl + 57203
3 libjvm.dylib 0x1a709dab JNI_CreateJavaVM_Impl + 56827
4 libjvm.dylib 0x1a709928 JNI_CreateJavaVM_Impl + 55672
5 libjvm.dylib 0x1a709588 JNI_CreateJavaVM_Impl + 54744
6 libjvm.dylib 0x1a71f931 jio_vsnprintf + 321
7 libjvm.dylib 0x1a71f86a jio_vsnprintf + 122
8 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
9 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
10 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 5: Java: Gang worker#1 (Parallel GC Threads)
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a709f23 JNI_CreateJavaVM_Impl + 57203
3 libjvm.dylib 0x1a709dab JNI_CreateJavaVM_Impl + 56827
4 libjvm.dylib 0x1a709928 JNI_CreateJavaVM_Impl + 55672
5 libjvm.dylib 0x1a709588 JNI_CreateJavaVM_Impl + 54744
6 libjvm.dylib 0x1a71f931 jio_vsnprintf + 321
7 libjvm.dylib 0x1a71f86a jio_vsnprintf + 122
8 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
9 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
10 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 6: Java: Concurrent Mark-Sweep GC Thread
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a70a037 JNI_CreateJavaVM_Impl + 57479
3 libjvm.dylib 0x1a726bb0 jio_vsnprintf + 29632
4 libjvm.dylib 0x1a7099b7 JNI_CreateJavaVM_Impl + 55815
5 libjvm.dylib 0x1a709588 JNI_CreateJavaVM_Impl + 54744
6 libjvm.dylib 0x1a7e3b8c JVM_Available + 29852
7 libjvm.dylib 0x1a726992 jio_vsnprintf + 29090
8 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
9 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
10 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 7: Java: VM Thread
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a70a037 JNI_CreateJavaVM_Impl + 57479
3 libjvm.dylib 0x1a726bb0 jio_vsnprintf + 29632
4 libjvm.dylib 0x1a7099b7 JNI_CreateJavaVM_Impl + 55815
5 libjvm.dylib 0x1a709588 JNI_CreateJavaVM_Impl + 54744
6 libjvm.dylib 0x1a79ef5b JVM_Lseek + 142763
7 libjvm.dylib 0x1a79ec8a JVM_Lseek + 142042
8 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
9 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
10 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 8: Java: Reference Handler
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a709f23 JNI_CreateJavaVM_Impl + 57203
3 libjvm.dylib 0x1a709dab JNI_CreateJavaVM_Impl + 56827
4 libjvm.dylib 0x1a7b3c95 JVM_MonitorWait + 5461
5 libjvm.dylib 0x1a7b2bfe JVM_MonitorWait + 1214
6 libjvm.dylib 0x1a7b287a JVM_MonitorWait + 314
7 ??? 0x1b80b839 0 + 461420601
8 ??? 0x1b803db1 0 + 461389233
9 ??? 0x1b803db1 0 + 461389233
10 ??? 0x1b8012d3 0 + 461378259
11 libjvm.dylib 0x1a7a07d0 JVM_Lseek + 149024
12 libjvm.dylib 0x1a7a0576 JVM_Lseek + 148422
13 libjvm.dylib 0x1a7b211b JVM_InternString + 2123
14 libjvm.dylib 0x1a7b1f8a JVM_InternString + 1722
15 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
16 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
17 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
18 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
19 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 9: Java: Finalizer
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a709f23 JNI_CreateJavaVM_Impl + 57203
3 libjvm.dylib 0x1a709dab JNI_CreateJavaVM_Impl + 56827
4 libjvm.dylib 0x1a7b3c95 JVM_MonitorWait + 5461
5 libjvm.dylib 0x1a7b2bfe JVM_MonitorWait + 1214
6 libjvm.dylib 0x1a7b287a JVM_MonitorWait + 314
7 ??? 0x1b80b839 0 + 461420601
8 ??? 0x1b9189e4 0 + 462522852
9 ??? 0x1b918694 0 + 462522004
10 ??? 0x1b803f17 0 + 461389591
11 ??? 0x1b8012d3 0 + 461378259
12 libjvm.dylib 0x1a7a07d0 JVM_Lseek + 149024
13 libjvm.dylib 0x1a7a0576 JVM_Lseek + 148422
14 libjvm.dylib 0x1a7b211b JVM_InternString + 2123
15 libjvm.dylib 0x1a7b1f8a JVM_InternString + 1722
16 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
17 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
18 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
19 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
20 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 10: Java: Surrogate Locker Thread (CMS)
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a709f23 JNI_CreateJavaVM_Impl + 57203
3 libjvm.dylib 0x1a709dab JNI_CreateJavaVM_Impl + 56827
4 libjvm.dylib 0x1a709928 JNI_CreateJavaVM_Impl + 55672
5 libjvm.dylib 0x1a7094a9 JNI_CreateJavaVM_Impl + 54521
6 libjvm.dylib 0x1a7c9097 JVM_IsPrimitiveClass + 7639
7 libjvm.dylib 0x1a7c8c11 JVM_IsPrimitiveClass + 6481
8 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
9 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
10 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
11 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
12 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 11: Java: Signal Dispatcher
0 libSystem.B.dylib 0x94c12916 semaphore_wait_trap + 10
1 libjvm.dylib 0x1a7c9b5e JVM_IsPrimitiveClass + 10398
2 libjvm.dylib 0x1a7c992e JVM_IsPrimitiveClass + 9838
3 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
4 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
5 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
6 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
7 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 12: Java: CompilerThread0
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a709f23 JNI_CreateJavaVM_Impl + 57203
3 libjvm.dylib 0x1a709dab JNI_CreateJavaVM_Impl + 56827
4 libjvm.dylib 0x1a709928 JNI_CreateJavaVM_Impl + 55672
5 libjvm.dylib 0x1a7094a9 JNI_CreateJavaVM_Impl + 54521
6 libjvm.dylib 0x1a7caec2 JVM_IsPrimitiveClass + 15362
7 libjvm.dylib 0x1a7cac9b JVM_IsPrimitiveClass + 14811
8 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
9 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
10 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
11 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
12 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 13: Java: Low Memory Detector
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a709f23 JNI_CreateJavaVM_Impl + 57203
3 libjvm.dylib 0x1a709dab JNI_CreateJavaVM_Impl + 56827
4 libjvm.dylib 0x1a709928 JNI_CreateJavaVM_Impl + 55672
5 libjvm.dylib 0x1a709588 JNI_CreateJavaVM_Impl + 54744
6 libjvm.dylib 0x1a7cee32 JVM_IsPrimitiveClass + 31602
7 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
8 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
9 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
10 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
11 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 14: Java: VM Periodic Task Thread
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a70a037 JNI_CreateJavaVM_Impl + 57479
3 libjvm.dylib 0x1a7d010d JVM_IsPrimitiveClass + 36429
4 libjvm.dylib 0x1a7cfcb3 JVM_IsPrimitiveClass + 35315
5 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
6 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
7 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 15: Java: Timer-0
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a70a037 JNI_CreateJavaVM_Impl + 57479
3 libjvm.dylib 0x1a726bb0 jio_vsnprintf + 29632
4 libjvm.dylib 0x1a7b38a8 JVM_MonitorWait + 4456
5 libjvm.dylib 0x1a7b2bfe JVM_MonitorWait + 1214
6 libjvm.dylib 0x1a7b287a JVM_MonitorWait + 314
7 ??? 0x1b80b839 0 + 461420601
8 ??? 0x1b803db1 0 + 461389233
9 ??? 0x1b803db1 0 + 461389233
10 ??? 0x1b8012d3 0 + 461378259
11 libjvm.dylib 0x1a7a07d0 JVM_Lseek + 149024
12 libjvm.dylib 0x1a7a0576 JVM_Lseek + 148422
13 libjvm.dylib 0x1a7b211b JVM_InternString + 2123
14 libjvm.dylib 0x1a7b1f8a JVM_InternString + 1722
15 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
16 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
17 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
18 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
19 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 16: Java: AWT-Shutdown
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a709f23 JNI_CreateJavaVM_Impl + 57203
3 libjvm.dylib 0x1a709dab JNI_CreateJavaVM_Impl + 56827
4 libjvm.dylib 0x1a7b3c95 JVM_MonitorWait + 5461
5 libjvm.dylib 0x1a7b2bfe JVM_MonitorWait + 1214
6 libjvm.dylib 0x1a7b287a JVM_MonitorWait + 314
7 ??? 0x1b80b839 0 + 461420601
8 ??? 0x1b803db1 0 + 461389233
9 ??? 0x1b803db1 0 + 461389233
10 ??? 0x1b80428d 0 + 461390477
11 ??? 0x1b8012d3 0 + 461378259
12 libjvm.dylib 0x1a7a07d0 JVM_Lseek + 149024
13 libjvm.dylib 0x1a7a0576 JVM_Lseek + 148422
14 libjvm.dylib 0x1a7b211b JVM_InternString + 2123
15 libjvm.dylib 0x1a7b1f8a JVM_InternString + 1722
16 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
17 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
18 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
19 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
20 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 17: Java: Java2D Disposer
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a709f23 JNI_CreateJavaVM_Impl + 57203
3 libjvm.dylib 0x1a709dab JNI_CreateJavaVM_Impl + 56827
4 libjvm.dylib 0x1a7b3c95 JVM_MonitorWait + 5461
5 libjvm.dylib 0x1a7b2bfe JVM_MonitorWait + 1214
6 libjvm.dylib 0x1a7b287a JVM_MonitorWait + 314
7 ??? 0x1b80b839 0 + 461420601
8 ??? 0x1b9189e4 0 + 462522852
9 ??? 0x1b918694 0 + 462522004
10 ??? 0x1b803f17 0 + 461389591
11 ??? 0x1b80428d 0 + 461390477
12 ??? 0x1b8012d3 0 + 461378259
13 libjvm.dylib 0x1a7a07d0 JVM_Lseek + 149024
14 libjvm.dylib 0x1a7a0576 JVM_Lseek + 148422
15 libjvm.dylib 0x1a7b211b JVM_InternString + 2123
16 libjvm.dylib 0x1a7b1f8a JVM_InternString + 1722
17 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
18 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
19 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
20 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
21 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 18: Java: AWT-EventQueue-0
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 com.apple.CoreGraphics 0x0555d5ea _CGSSynchronizeWindowBackingStore + 139
3 com.apple.CoreGraphics 0x05556770 _CGSLockWindow + 5001
4 com.apple.CoreGraphics 0x0555d18a CGSDeviceLock + 493
5 libRIP.A.dylib 0x9537258b ripd_Lock + 62
6 libRIP.A.dylib 0x95371e88 ripl_BltShape + 599
7 libRIP.A.dylib 0x9536f23f ripc_Render + 377
8 libRIP.A.dylib 0x9537e18a ripc_DrawPath + 577
9 com.apple.CoreGraphics 0x055decaf CGContextDrawPath + 176
10 com.apple.CoreGraphics 0x055debfa CGContextFillPath + 25
11 libawt.jnilib 0x2632dd80 CompleteCGContext + 126
12 libawt.jnilib 0x2632dc90 ViewSD_finishCGContext + 176
13 libawt.jnilib 0x2632b55e Java_apple_awt_CRenderer_doRect + 406
14 ??? 0x1b80b839 0 + 461420601
15 ??? 0x1b803db1 0 + 461389233
16 ??? 0x1b803db1 0 + 461389233
17 ??? 0x1b803db1 0 + 461389233
18 ??? 0x1b80428d 0 + 461390477
19 ??? 0x1b80428d 0 + 461390477
20 ??? 0x1b803db1 0 + 461389233
21 ??? 0x1b803db1 0 + 461389233
22 ??? 0x1b803db1 0 + 461389233
23 ??? 0x1b9b390c 0 + 463157516
24 ??? 0x1b803db1 0 + 461389233
25 ??? 0x1b803db1 0 + 461389233
26 ??? 0x1b803db1 0 + 461389233
27 ??? 0x1b803db1 0 + 461389233
28 ??? 0x1b803db1 0 + 461389233
29 ??? 0x1b80428d 0 + 461390477
30 ??? 0x1b80428d 0 + 461390477
31 ??? 0x1b9be2b0 0 + 463200944
32 ??? 0x1b803fdd 0 + 461389789
33 ??? 0x1b803db1 0 + 461389233
34 ??? 0x1b803db1 0 + 461389233
35 ??? 0x1b803db1 0 + 461389233
36 ??? 0x1b803db1 0 + 461389233
37 ??? 0x1b8012d3 0 + 461378259
38 libjvm.dylib 0x1a7a07d0 JVM_Lseek + 149024
39 libjvm.dylib 0x1a7a0576 JVM_Lseek + 148422
40 libjvm.dylib 0x1a7b211b JVM_InternString + 2123
41 libjvm.dylib 0x1a7b1f8a JVM_InternString + 1722
42 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
43 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
44 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
45 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
46 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 19: Java: TimerQueue
0 libSystem.B.dylib 0x94c128da mach_msg_trap + 10
1 libSystem.B.dylib 0x94c13047 mach_msg + 68
2 libjvm.dylib 0x1a70a037 JNI_CreateJavaVM_Impl + 57479
3 libjvm.dylib 0x1a726bb0 jio_vsnprintf + 29632
4 libjvm.dylib 0x1a7b38a8 JVM_MonitorWait + 4456
5 libjvm.dylib 0x1a7b2bfe JVM_MonitorWait + 1214
6 libjvm.dylib 0x1a7b287a JVM_MonitorWait + 314
7 ??? 0x1b80b839 0 + 461420601
8 ??? 0x1b803db1 0 + 461389233
9 ??? 0x1b80428d 0 + 461390477
10 ??? 0x1b8012d3 0 + 461378259
11 libjvm.dylib 0x1a7a07d0 JVM_Lseek + 149024
12 libjvm.dylib 0x1a7a0576 JVM_Lseek + 148422
13 libjvm.dylib 0x1a7b211b JVM_InternString + 2123
14 libjvm.dylib 0x1a7b1f8a JVM_InternString + 1722
15 libjvm.dylib 0x1a7b1d74 JVM_InternString + 1188
16 libjvm.dylib 0x1a7b180f JVM_StartThread + 2175
17 libjvm.dylib 0x1a70933b JNI_CreateJavaVM_Impl + 54155
18 libSystem.B.dylib 0x94c3ffbd _pthread_start + 345
19 libSystem.B.dylib 0x94c3fe42 thread_start + 34

Thread 2 crashed with X86 Thread State (32-bit):
eax: 0x0000003c ebx: 0x94c7f899 ecx: 0xb10f289c edx: 0x94c7fa4e
edi: 0xa0719b10 esi: 0xb10f28f8 ebp: 0xb10f28d8 esp: 0xb10f289c
ss: 0x0000001f efl: 0x00000247 eip: 0x94c7fa4e cs: 0x00000007
ds: 0x0000001f es: 0x0000001f fs: 0x0000001f gs: 0x00000037
cr2: 0x1b800100

Model: MacBook6,1, BootROM MB61.00C8.B00, 2 processors, Intel Core 2 Duo, 2.26 GHz, 4 GB, SMC 1.51f53
Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x93), Broadcom BCM43xx 1.0 (5.10.131.1 )
Bluetooth: Version 2.2.4f3, 2 service, 1 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Serial ATA Device: Hitachi HTS545025B9SA02, 232.89 GB
Serial ATA Device: MATSHITADVD-R UJ-898
USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8507, 0x24400000
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x0236, 0x04600000
USB Device: BRCM2070 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x06100000
USB Device: Bluetooth Module, 0x05ac (Apple Inc.), 0x8218, 0x06130000

Thanks for your help!
Erin

Hi Erin,

It appears Matlab is crashing. This could be a bit difficult to track down- is there a reason you need to use the Developer’s and not the compiled version? Also, we have a new version of CellProfiler, CP 2.0, which does away with all the Matlab problems by being in Python!

Additionally, we have released a couple of times since 5811, and there have been many bugfixes. I would recommend downloading a newer version of CP- preferably CP 2.0, since its easier to work with. If you really need the Matlab functionality (that is, you plan to/have already written your own Matlab CP modules) let us know and we can try to help you debug further- but likely this is related to your Matlab installation only, and not CP.

~kate

Hi Kate,

Thanks for the quick response! I’m using a series of preexisting pipelines in 5811, as well as working with a team that is all using 5811 so I’d rather not switch versions. I’m sure you’re right and it is the MATLAb installation that has the problem - Any ideas on where I could start trying to find / fix the problem? I’ve tried deleting MATLAB and reinstalling it.

Thanks for your help!

Erin

Hi Erin,

I suspect that it is a problem with Snow Leopard (OS 10.6) & Matlab74 incompatibility. For example, see this thread:
mathworks.in/matlabcentral/n … ead/274183
Does Matlab work otherwise for you on this machine?

We haven’t tried CellProfiler on Snow Leopard with older versions of CellProfiler, so you’re treading on new ground.

David

Thanks for your help last year guys!

Regarding the above messages, I ended up solving that MatLab issue by switching to an older computer which was able to run MatLab 2007a successfully. However, as old computers tend to do, mine stopped working, so I’m back at trying to fix the CP start-up issue! I’d like to continue using 5811 for now, but I’ve switched versions of MatLab to version R2011a, and now I’m getting a new error, which seems to be easier to deal with than the last (or at least shorter):

>> run ‘/Applications/CellProfiler/CellProfiler.m’

??? Error: File: system_dependent.m Line: 1 Column: 25
The input character is not valid in MATLAB statements or
expressions.
Error in ==> usejava at 47
isok = system_dependent(‘useJava’,feature);
Error in ==> CPdynamizescrollbar at 5
if usejava(‘awt’),
Error in ==> CellProfiler>CellProfiler_LayoutFcn at 5710
CPdynamizescrollbar(h12);
Error in ==> CellProfiler>gui_mainfcn at 6079
gui_hFigure = feval(gui_State.gui_LayoutFcn,
gui_SingletonOpt);
Error in ==> CellProfiler at 55
gui_mainfcn(gui_State, varargin{:});
Error in ==> run at 57
evalin(‘caller’, [s ‘;’]);

Has anyone seen this before, or have any tips on how to fix it?

Thanks!

-Erin

Hi Erin,

Not quite sure what the issue is, but can you confirm that when you run this command at the Matlab prompt:

you get this?

[quote]isok =

 1[/quote]

Also, is Java installed on your new machine? (You can test it here: java.com/en/download/index.jsp)

-David

Hi David!

I do indeed get an answer of 1 using that command! Also I seem to have fixed the problem by accident, by deleting CP and re-downloading it. Now it works - I’m not sure why but I’m happy!

Thanks for your feedback!

-Erin

Ah, good!
-David