[Rd] Double free or memory corruption problem (PR#9125)

clwang at yahoo-inc.com clwang at yahoo-inc.com
Fri Aug 4 20:06:46 CEST 2006


Full_Name: Clem Wang
Version: 1.14 (v2129)
OS: Mac OS X 10.3.9
Submission from: (NULL) (216.145.49.15)


I did a bunch of boxplots with commands like:
# the class is in column 1
par(mfrow=c(8,6))
for(i in 2:length(s.df)){
boxplot(split(log(s.df[i]+1),
s.df$CLASS),ylab="CLASS"),xlab=names(s.df[i]),horizontal=T);
}

the dataframe contains about 50,000 rows, 50 columns.  the Class (in column 1)
has two values: 0 and 1 

The I switch to other applications (Firefox, terminal) and left my computer on
over night.  When I returned to R, i discovered a number of err msgs for a
number of different addresses:

"Deallocation of a pointer no malloced: (some address); This could be a double
free(), or free() called with the middle of an allocataed block; Try setting
environment variable MallocHelp to see tools to help debug"

The redrawing of my windows became VERY slow and eventually I crashed (see
below.)

I will try to reproduce this, but I'm not sure that I can.  (I reporting this
now so I don't lose the Apple Crash Report.)

I have 1 GB of Ram running on a 1.33 GHz PowerPC G4.


===============================================================
Date/Time:      2006-08-04 10:47:27 -0700
OS Version:     10.3.9 (Build 7W98)
Report Version: 2

Command: R
Path:    /Applications/R.app/Contents/MacOS/R
Version: 1.14 (2129)
PID:     496
Thread:  0

Exception:  EXC_BAD_ACCESS (0x0001)
Codes:      KERN_PROTECTION_FAILURE (0x0002) at 0x00000005

Thread 0 Crashed:
0   libR.dylib               	0x01059ab4 GEsystemState + 0xc (engine.c:134)
1   libR.dylib               	0x0101d99c Rf_gpptr + 0x24 (base.c:174)
2   libR.dylib               	0x01080264 xDevtoNDCUnits + 0x1c (graphics.c:221)
3   libR.dylib               	0x01080514 xDevtoInchUnits + 0x1c
(graphics.c:270)
4   libR.dylib               	0x010808d8 Rf_GConvertXUnits + 0x1c8
(graphics.c:333)
5   libR.dylib               	0x01088824 Rf_GStrWidth + 0x54 (graphics.c:2922)
6   libR.dylib               	0x010b8474 do_axis + 0x1220 (plot.c:1393)
7   libR.dylib               	0x0105dffc GEplayDisplayList + 0xf0
(engine.c:2433)
8   org.R-project.R          	0x00016874 RQuartz_DiplayGList + 0x114
9   org.R-project.R          	0x00018fb4 -[RDeviceView drawRect:] + 0x118
10  org.R-project.R          	0x00015d78 -[RQuartz applicationDidUnhide:] +
0x58
11  com.apple.Foundation     	0x90a27a94 _nsnote_callback + 0xb0
12  com.apple.CoreFoundation 	0x901db118 __CFXNotificationPost + 0x1b4
13  com.apple.CoreFoundation 	0x901dfb7c _CFXNotificationPostNotification +
0x340
14  com.apple.Foundation     	0x90a258e0 -[NSNotificationCenter
postNotificationName:object:userInfo:] + 0x74
15  com.apple.AppKit         	0x9303e724 -[NSApplication
_doUnhideWithoutActivation] + 0x1f0
16  com.apple.AppKit         	0x9303e4b8 _hideShowHandler + 0x9c
17  com.apple.HIToolbox      	0x9809ae50 DispatchEventToHandlers + 0x150
18  com.apple.HIToolbox      	0x9809b0c4 SendEventToEventTargetInternal + 0x174
19  com.apple.HIToolbox      	0x980ad530 SendEventToEventTarget + 0x28
20  com.apple.AppKit         	0x92e824a0 _DPSNextEvent + 0x3c8
21  com.apple.AppKit         	0x92e98cd8 -[NSApplication
nextEventMatchingMask:untilDate:inMode:dequeue:] + 0x74
22  org.R-project.R          	0x00009280 -[RController doProcessEvents:] + 0x60
23  org.R-project.R          	0x00005cc0 -[RController handleReadConsole:] +
0x54
24  org.R-project.R          	0x0000be44 Re_ReadConsole + 0x74
25  org.R-project.R          	0x00015700 RGUI_ReplIteration + 0x70
26  org.R-project.R          	0x00015674 RGUI_ReplConsole + 0x94
27  org.R-project.R          	0x000155c8 run_REngineRmainloop + 0x9c
28  org.R-project.R          	0x0000e56c -[REngine runREPL] + 0x4c
29  com.apple.Foundation     	0x90a239f4 __NSFireTimer + 0x68
30  com.apple.CoreFoundation 	0x901c5170 __CFRunLoopDoTimer + 0xf4
31  com.apple.CoreFoundation 	0x901c24d0 __CFRunLoopRun + 0x5c8
32  com.apple.CoreFoundation 	0x901c69e4 CFRunLoopRunSpecific + 0x148
33  com.apple.HIToolbox      	0x9809ee10 RunCurrentEventLoopInMode + 0xac
34  com.apple.HIToolbox      	0x980a553c ReceiveNextEventCommon + 0x17c
35  com.apple.HIToolbox      	0x980c7638 BlockUntilNextEventMatchingListInMode +
0x60
36  com.apple.AppKit         	0x92e82258 _DPSNextEvent + 0x180
37  com.apple.AppKit         	0x92e98cd8 -[NSApplication
nextEventMatchingMask:untilDate:inMode:dequeue:] + 0x74
38  com.apple.AppKit         	0x92ead058 -[NSApplication run] + 0x21c
39  com.apple.AppKit         	0x92f69774 NSApplicationMain + 0x1d0
40  org.R-project.R          	0x00002eb0 _start + 0x188 (crt.c:267)
41  dyld                     	0x8fe1a278 _dyld_start + 0x64

Thread 1:
0   libSystem.B.dylib        	0x900078b8 mach_msg_trap + 0x8
1   libSystem.B.dylib        	0x90007438 mach_msg + 0x38
2   com.unsanity.ape         	0xc00024ec __ape_internal + 0xca4
3   com.unsanity.ape         	0xc0001340 __ape_agent + 0x40
4   libSystem.B.dylib        	0x90024990 _pthread_body + 0x28

Thread 2:
0   libSystem.B.dylib        	0x9000b46c select + 0xc
1   org.R-project.R          	0x00004674 -[RController readThread:] + 0x20c
2   com.apple.Foundation     	0x90a6a4b8 forkThreadForFunction + 0x6c
3   libSystem.B.dylib        	0x90024990 _pthread_body + 0x28

Thread 3:
0   libSystem.B.dylib        	0x90017238 semaphore_wait_signal_trap + 0x8
1   libSystem.B.dylib        	0x9000ea1c _pthread_cond_wait + 0x270
2   com.apple.Foundation     	0x90a7c598 -[NSConditionLock lockWhenCondition:] +
0x44
3   com.apple.AppKit         	0x92e7a0f8 -[NSUIHeartBeat _heartBeatThread:] +
0x190
4   com.apple.Foundation     	0x90a6a4b8 forkThreadForFunction + 0x6c
5   libSystem.B.dylib        	0x90024990 _pthread_body + 0x28

Thread 4:
0   libSystem.B.dylib        	0x900078b8 mach_msg_trap + 0x8
1   libSystem.B.dylib        	0x90007438 mach_msg + 0x38
2   com.apple.CoreFoundation 	0x901c2258 __CFRunLoopRun + 0x350
3   com.apple.CoreFoundation 	0x901c69e4 CFRunLoopRunSpecific + 0x148
4   com.apple.Foundation     	0x90a2d160 -[NSRunLoop runMode:beforeDate:] +
0xac
5   com.apple.Foundation     	0x90a45d64 -[NSRunLoop run] + 0x4c
6   com.apple.Foundation     	0x90a97ffc
+[NSURLConnection(NSURLConnectionInternal) _resourceLoadLoop:] + 0x20c
7   com.apple.Foundation     	0x90a6a4b8 forkThreadForFunction + 0x6c
8   libSystem.B.dylib        	0x90024990 _pthread_body + 0x28

Thread 5:
0   libSystem.B.dylib        	0x900078b8 mach_msg_trap + 0x8
1   libSystem.B.dylib        	0x90007438 mach_msg + 0x38
2   com.apple.CoreFoundation 	0x901c2258 __CFRunLoopRun + 0x350
3   com.apple.CoreFoundation 	0x901c69e4 CFRunLoopRunSpecific + 0x148
4   com.apple.Foundation     	0x90a2d160 -[NSRunLoop runMode:beforeDate:] +
0xac
5   com.apple.Foundation     	0x90a45d64 -[NSRunLoop run] + 0x4c
6   com.apple.Foundation     	0x90a9853c +[NSURLCache _diskCacheSyncLoop:] +
0xa8
7   com.apple.Foundation     	0x90a6a4b8 forkThreadForFunction + 0x6c
8   libSystem.B.dylib        	0x90024990 _pthread_body + 0x28

Thread 6:
0   libSystem.B.dylib        	0x900078b8 mach_msg_trap + 0x8
1   libSystem.B.dylib        	0x90007438 mach_msg + 0x38
2   com.apple.CoreFoundation 	0x901c2258 __CFRunLoopRun + 0x350
3   com.apple.CoreFoundation 	0x901c69e4 CFRunLoopRunSpecific + 0x148
4   com.apple.Foundation     	0x90a2d160 -[NSRunLoop runMode:beforeDate:] +
0xac
5   com.apple.Foundation     	0x90a45d64 -[NSRunLoop run] + 0x4c
6   com.apple.WebKit         	0x98ee5124 +[WebFileDatabase _syncLoop:] + 0xa8
7   com.apple.Foundation     	0x90a6a4b8 forkThreadForFunction + 0x6c
8   libSystem.B.dylib        	0x90024990 _pthread_body + 0x28

PPC Thread State:
  srr0: 0x01059ab4 srr1: 0x0000d030                vrsave: 0x00000000
    cr: 0x24422248  xer: 0x20000002   lr: 0x0101d99c  ctr: 0x01059aa8
    r0: 0x0101d99c   r1: 0xbfffd1e0   r2: 0x00000005   r3: 0x55b09430
    r4: 0x55b09430   r5: 0x55b09430   r6: 0x0000000d   r7: 0x55b09430
    r8: 0x41700000   r9: 0x00000034  r10: 0x00000000  r11: 0x011a7158
   r12: 0x01059aa8  r13: 0x44422228  r14: 0x00000001  r15: 0x16f10388
   r16: 0xbff00000  r17: 0x00000000  r18: 0x0ec91cd0  r19: 0x01ee84e8
   r20: 0x0e8c6b68  r21: 0x00000002  r22: 0x00000001  r23: 0x00000010
   r24: 0x00000002  r25: 0x0a0e2d78  r26: 0x55b09430  r27: 0x00000002
   r28: 0x0000000d  r29: 0x55b09430  r30: 0x55b09430  r31: 0x0101d980

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0xc0000000 - 0xc000efff com.unsanity.ape 1.4.5
/Library/Frameworks/ApplicationEnhancer.framework/Versions/A/ApplicationEnhancer



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