[R-SIG-Mac] R 2.10.0 instability (G5 iMac, Tiger 10.4.11)

Lawrie Conole lconole at gmail.com
Fri Nov 13 01:33:28 CET 2009


I've been trying to use R 2.10.0 in Tiger on a G5 iMac, but it
repeatedly crashes and I went back to 2.9.2 - no problems.  Reinstalled
2.10.0 and away we go crashing again.  Whilst I have quite a bit of 
experience in using R, I know next to nothing about 'under the hood' 
aspects, so de-bugging this is probably beyond me.

Today I'm trying to run the small co.var script that I wrote (below), 
which worked OK for a little while, then crashed R every time.

Back to 2.9.2 ...

I've included the sessionInfo() and crashlog(s), below the co.var script


_______________________________

co.var<-function(x)(100*sd(x)/mean(x))
co.var(x)

_______________________________

R version 2.10.0 (2009-10-26)
powerpc-apple-darwin8.11.1

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

______________________________

Mac OS X Version 10.4.11 (Build 8S165)
2009-11-13 08:28:12 +1100
2009-11-13 08:28:21.644 SystemUIServer[185] lang is:en
2009-11-13 08:28:23.111 SystemUIServer[185] Normally SSMenuExtra would
not have been loaded as a Menu Extra.
Workaround Bonjour: Unknown error: 0
Warning: unrecognized command line flag -psn_0_1966081
Warning: unrecognized command line flag -psn_0_2490369
Debugger() was called!
Debugger() was called!
Debugger() was called!
Warning: unrecognized command line flag -psn_0_3145729
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
FSCopyObject -- err: 0, maxLevels: 1, whichInfo: 00000000,
            dupeAction: ignore, wantSpec: no, wantName: no,
            filterProcPtr: 0x00000000, yourDataPtr: 0x00000000,
            newObjectRef: 0xbfffed08, newObjectSpec: 0x00000000,
            copyBufferSize: 256kB, isDirectory: no, isLocal: yes,
            isDropBox: no, PBHCopyFileSync supported: no

FSCopyObject -- err: 0, maxLevels: 1, whichInfo: 00000000,
            dupeAction: ignore, wantSpec: no, wantName: no,
            filterProcPtr: 0x00000000, yourDataPtr: 0x00000000,
            newObjectRef: 0xbfffed08, newObjectSpec: 0x00000000,
            copyBufferSize: 256kB, isDirectory: no, isLocal: yes,
            isDropBox: no, PBHCopyFileSync supported: no

Debugger() was called!
Debugger() was called!
Debugger() was called!
Debugger() was called!
Nov 13 10:51:08 lawrie-conoles-imac-g5 crashdump[282]: R crashed
Nov 13 10:51:13 lawrie-conoles-imac-g5 crashdump[282]: crash report
written to: /Users/lawrieconole/Library/Logs/CrashReporter/R.crash.log
Nov 13 10:52:23 lawrie-conoles-imac-g5 crashdump[286]: R crashed
Nov 13 10:52:27 lawrie-conoles-imac-g5 crashdump[286]: crash report
written to: /Users/lawrieconole/Library/Logs/CrashReporter/R.crash.log
Nov 13 10:57:01 lawrie-conoles-imac-g5 crashdump[295]: R crashed
Nov 13 10:57:05 lawrie-conoles-imac-g5 crashdump[295]: crash report
written to: /Users/lawrieconole/Library/Logs/CrashReporter/R.crash.log
Nov 13 10:58:55 lawrie-conoles-imac-g5 crashdump[300]: R crashed
Nov 13 10:58:59 lawrie-conoles-imac-g5 crashdump[300]: crash report
written to: /Users/lawrieconole/Library/Logs/CrashReporter/R.crash.log
Nov 13 11:00:13 lawrie-conoles-imac-g5 crashdump[306]: R crashed
Nov 13 11:00:18 lawrie-conoles-imac-g5 crashdump[306]: crash report
written to: /Users/lawrieconole/Library/Logs/CrashReporter/R.crash.log


______________________________




Date/Time:      2009-11-13 11:00:11.795 +1100
OS Version:     10.4.11 (Build 8S165)
Report Version: 4

Command: R
Path:    /Applications/R.app/Contents/MacOS/R
Parent:  WindowServer [64]

Version: R 2.9.2 GUI 1.29 Tiger build 32-bit (5511)

PID:    305
Thread: 0

Exception:  EXC_BAD_ACCESS (0x0001)
Codes:      KERN_PROTECTION_FAILURE (0x0002) at 0x00000020

Thread 0 Crashed:
0   libobjc.A.dylib              0x90a410f8 objc_msgSend + 24
1   org.R-project.R              0x0000dae4 Re_RBusy + 60 (Rcallbacks.m:178)
2   libR.dylib                   0x003cdcf0 R_ReplDLLdo1 + 64
3   org.R-project.R              0x00018358 run_REngineRmainloop + 368
(Rinit.m:521)
4   org.R-project.R              0x00010a0c -[REngine runREPL] + 484
(REngine.m:181)
5   org.R-project.R              0x00002a38 main + 1040 (main.m:140)
6   org.R-project.R              0x000025ac _start + 760
7   org.R-project.R              0x000022b0 start + 48

Thread 1:
0   libSystem.B.dylib            0x9000af48 mach_msg_trap + 8
1   libSystem.B.dylib            0x9000ae9c mach_msg + 60
2   com.apple.CoreFoundation     0x907de9ac __CFRunLoopRun + 832
3   com.apple.CoreFoundation     0x907de2b0 CFRunLoopRunSpecific + 268
4   com.apple.Foundation         0x92c0fb7c +[NSURLCache
_diskCacheSyncLoop:] + 152
5   com.apple.Foundation         0x92be74d8 forkThreadForFunction + 108
6   libSystem.B.dylib            0x9002b908 _pthread_body + 96

Thread 2:
0   libSystem.B.dylib            0x9000af48 mach_msg_trap + 8
1   libSystem.B.dylib            0x9000ae9c mach_msg + 60
2   com.apple.CoreFoundation     0x907de9ac __CFRunLoopRun + 832
3   com.apple.CoreFoundation     0x907de2b0 CFRunLoopRunSpecific + 268
4   com.apple.Foundation         0x92bdc8dc -[NSConnection
sendInvocation:] + 1468
5   com.apple.Foundation         0x92bdb378
-[NSObject(NSForwardInvocation) forward::] + 408
6   libobjc.A.dylib              0x90a460b0 _objc_msgForward + 176
7   com.apple.Foundation         0x92bdb6e0 -[NSDistantObject
methodSignatureForSelector:] + 268
8   com.apple.Foundation         0x92bdb248
-[NSObject(NSForwardInvocation) forward::] + 104
9   libobjc.A.dylib              0x90a460b0 _objc_msgForward + 176
10  org.R-project.R              0x00005068 -[RController readThread:] +
2908 (RController.m:747)
11  com.apple.Foundation         0x92be74d8 forkThreadForFunction + 108
12  libSystem.B.dylib            0x9002b908 _pthread_body + 96

Thread 3:
0   libSystem.B.dylib            0x9004a2e8 syscall_thread_switch + 8
1   com.apple.Foundation         0x92bff940 +[NSThread sleepUntilDate:]
+ 152
2   com.apple.AppKit             0x9382f660 -[NSUIHeartBeat
_heartBeatThread:] + 1100
3   com.apple.Foundation         0x92be74d8 forkThreadForFunction + 108
4   libSystem.B.dylib            0x9002b908 _pthread_body + 96

Thread 0 crashed with PPC Thread State 64:
  srr0: 0x0000000090a410f8 srr1:
0x100000000200f030                        vrsave: 0x0000000000000000
    cr: 0x44000482          xer: 0x0000000000000000   lr:
0x000000000000dae4  ctr: 0x0000000090a410e0
    r0: 0x00000000003cdcf0   r1: 0x00000000bffff4a0   r2:
0x0000000000000000   r3: 0x00000000a0a3c864
    r4: 0x0000000000037114   r5: 0x0000000000000060   r6:
0xfffffffffffffff9   r7: 0x0000000000000003
    r8: 0x0000000030393000   r9: 0x00000000005808ac  r10:
0x0000000000478cd8  r11: 0x00000000fffd7114
   r12: 0x0000000000000000  r13: 0x0000000000000000  r14:
0x0000000000000000  r15: 0x0000000002307cf0
   r16: 0x00000000000430ac  r17: 0x0000000000042388  r18:
0x00000000a378a078  r19: 0x00000000000430a8
   r20: 0x0000000000042370  r21: 0x0000000000043094  r22:
0x000000000004238c  r23: 0x0000000000042358
   r24: 0x000000000004309c  r25: 0x0000000000042350  r26:
0x000000000231d4c0  r27: 0x00000000028b4c38
   r28: 0x0000000000000000  r29: 0x000000000003e020  r30:
0x000000000057dcbc  r31: 0x00000000003cdcbc

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0x94519000 - 0x94556fff libsqlite3.0.dylib     /usr/lib/libsqlite3.0.dylib
0x9455e000 - 0x945aefff libGLImage.dylib
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x945b7000 - 0x945d0fff com.apple.CoreVideo 1.4.2
/System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
0x9477e000 - 0x9478dfff libCGATS.A.dylib
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGATS.A.dylib
0x94795000 - 0x947a2fff libCSync.A.dylib
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCSync.A.dylib
0x947e8000 - 0x94801fff libRIP.A.dylib
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib
0x94c23000 - 0x94c94fff libstdc++.6.dylib     /usr/lib/libstdc++.6.dylib
0x95b42000 - 0x95b44fff com.apple.ExceptionHandling 1.2 (???)
/System/Library/Frameworks/ExceptionHandling.framework/Versions/A/ExceptionHandling
0x9608b000 - 0x960b9fff libncurses.5.4.dylib
/usr/lib/libncurses.5.4.dylib
0x96a01000 - 0x96a20fff com.apple.vecLib 3.2.2 (vecLib 3.2.2)
/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
0x9b8c0000 - 0x9b8e1fff libmx.A.dylib     /usr/lib/libmx.A.dylib

Model: PowerMac8,1, BootROM 5.2.2f4, 1 processors, PowerPC G5  (3.0),
1.8 GHz, 1.25 GB
Graphics: GeForce FX 5200, GeForce FX 5200, AGP, 64 MB
Memory Module: DIMM0/J4000, 256 MB, DDR SDRAM, PC3200U-30330
Memory Module: DIMM1/J4001, 1 GB, DDR SDRAM, PC3200U-30330
Modem: Jump, V.92, Version 1.0
Network Service: Built-in Ethernet, Ethernet, en0
Serial ATA Device: ST380013AS, 74.53 GB
Parallel ATA Device: MATSHITADVD-R   UJ-825
USB Device: USB2.0 Hub Controller, NEC Corporation, Up to 480 Mb/sec, 500 mA
USB Device: Hub in Apple Pro Keyboard, Mitsumi Electric, Up to 12
Mb/sec, 500 mA
USB Device: USB-PS/2 Optical Mouse, Logitech, Up to 1.5 Mb/sec, 100 mA
USB Device: Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, 250 mA




-- 
Lawrie Conole
28 Reid Street
Northcote 3070
lconole[at]gmail.com
03 9410 9384
0419 588 993



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