Re: [R] segmentation fault with Hmisc areg.boot(): Now acepack avas failure

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri 17 Feb 2006 - 09:02:02 EST

This is a problem in a contributed package, and probably in your OS only as the daily package checks on Linux and Windows are not reporting errors.

The posting guide suggested contacting the maintainer. As he has a Mac, he may be able to help.

On Thu, 16 Feb 2006, Martin Henry H. Stevens wrote:

> Hi Folks,
> Mac OS 10.4.4
> R 2.2.1(2005-12-20 r36812)
> Hmisc 3.0-10
> acepack 1.3-2.2
>
> I had R crashes while running areg.boot in Hmisc (see old message
> below), but now I realize that the problem appears to be in the avas
> function in acepack. I tried running running the avas example (in
> acepack package), and got an immediate crash.
>
> Any thoughts? The Apple crash report (from R GUI crash) follows.
>
> Hank
> Date/Time: 2006-02-16 14:28:39.836 -0500
> OS Version: 10.4.4 (Build 8G32)
> Report Version: 3
>
> Command: R
> Path: /Applications/R.app/Contents/MacOS/R
> Parent: WindowServer [75]
>
> Version: 1.14 (2129)
>
> PID: 1814
> Thread: 0
>
> Exception: EXC_BAD_ACCESS (0x0001)
> Codes: KERN_INVALID_ADDRESS (0x0001) at 0xfb3513df
>
> Thread 0 Crashed:
> 0 acepack.so 0x067c42c0 avas_ + 1752 (avas.f:112)
> 1 libR.dylib 0x0024f498 do_dotCode + 1844 (dotcode.c:
> 1722)
> 2 libR.dylib 0x00265cb0 Rf_eval + 1544 (eval.c:405)
> 3 libR.dylib 0x00267ccc do_set + 224 (eval.c:1309)
> 4 libR.dylib 0x00265af4 Rf_eval + 1100 (eval.c:382)
> 5 libR.dylib 0x0026744c do_begin + 136 (eval.c:1058)
> 6 libR.dylib 0x00265af4 Rf_eval + 1100 (eval.c:382)
> 7 libR.dylib 0x00266150 Rf_applyClosure + 952
> (eval.c:576)
> 8 libR.dylib 0x00265d2c Rf_eval + 1668 (eval.c:417)
> 9 libR.dylib 0x00267ccc do_set + 224 (eval.c:1309)
> 10 libR.dylib 0x00265af4 Rf_eval + 1100 (eval.c:382)
> 11 org.R-project.R 0x00015884 RGUI_ReplIteration + 500
> (crt.c:300)
> 12 org.R-project.R 0x00015674 RGUI_ReplConsole + 148
> (crt.c:300)
> 13 org.R-project.R 0x000155c8 run_REngineRmainloop + 156
> (crt.c:300)
> 14 org.R-project.R 0x0000e56c -[REngine runREPL] + 76
> (crt.c:300)
> 15 com.apple.Foundation 0x928e949c __NSFireTimer + 116
> 16 com.apple.CoreFoundation 0x90770aec __CFRunLoopDoTimer + 184
> 17 com.apple.CoreFoundation 0x9075d464 __CFRunLoopRun + 1680
> 18 com.apple.CoreFoundation 0x9075ca18 CFRunLoopRunSpecific + 268
> 19 com.apple.HIToolbox 0x9318e1e0 RunCurrentEventLoopInMode + 264
> 20 com.apple.HIToolbox 0x9318d874 ReceiveNextEventCommon + 380
> 21 com.apple.HIToolbox 0x9318d6e0
> BlockUntilNextEventMatchingListInMode + 96
> 22 com.apple.AppKit 0x9368b104 _DPSNextEvent + 384
> 23 com.apple.AppKit 0x9368adc8 -[NSApplication
> nextEventMatchingMask:untilDate:inMode:dequeue:] + 116
> 24 com.apple.AppKit 0x9368730c -[NSApplication run] + 472
> 25 com.apple.AppKit 0x93777e68 NSApplicationMain + 452
> 26 org.R-project.R 0x00002eb0 _start + 392 (crt.c:267)
> 27 dyld 0x8fe01048 _dyld_start + 60
>
> Thread 1:
> 0 libSystem.B.dylib 0x9001f20c select + 12
> 1 org.R-project.R 0x00004674 -[RController readThread:] +
> 524 (crt.c:300)
> 2 com.apple.Foundation 0x928e66d4 forkThreadForFunction + 108
> 3 libSystem.B.dylib 0x9002b200 _pthread_body + 96
>
> Thread 2:
> 0 libSystem.B.dylib 0x90049748 syscall_thread_switch + 8
> 1 com.apple.Foundation 0x928fead0 +[NSThread sleepUntilDate:]
> + 152
> 2 com.apple.AppKit 0x93728034 -[NSUIHeartBeat
> _heartBeatThread:] + 1100
> 3 com.apple.Foundation 0x928e66d4 forkThreadForFunction + 108
> 4 libSystem.B.dylib 0x9002b200 _pthread_body + 96
>
> Thread 3:
> 0 libSystem.B.dylib 0x9000b208 mach_msg_trap + 8
> 1 libSystem.B.dylib 0x9000b15c mach_msg + 60
> 2 com.apple.CoreFoundation 0x9075d114 __CFRunLoopRun + 832
> 3 com.apple.CoreFoundation 0x9075ca18 CFRunLoopRunSpecific + 268
> 4 com.apple.Foundation 0x9290db9c +[NSURLConnection
> (NSURLConnectionInternal) _resourceLoadLoop:] + 264
> 5 com.apple.Foundation 0x928e66d4 forkThreadForFunction + 108
> 6 libSystem.B.dylib 0x9002b200 _pthread_body + 96
>
> Thread 4:
> 0 libSystem.B.dylib 0x9000b208 mach_msg_trap + 8
> 1 libSystem.B.dylib 0x9000b15c mach_msg + 60
> 2 com.apple.CoreFoundation 0x9075d114 __CFRunLoopRun + 832
> 3 com.apple.CoreFoundation 0x9075ca18 CFRunLoopRunSpecific + 268
> 4 com.apple.Foundation 0x9290ecdc +[NSURLCache
> _diskCacheSyncLoop:] + 152
> 5 com.apple.Foundation 0x928e66d4 forkThreadForFunction + 108
> 6 libSystem.B.dylib 0x9002b200 _pthread_body + 96
>
> Thread 5:
> 0 libSystem.B.dylib 0x9000b208 mach_msg_trap + 8
> 1 libSystem.B.dylib 0x9000b15c mach_msg + 60
> 2 com.apple.CoreFoundation 0x9075d114 __CFRunLoopRun + 832
> 3 com.apple.CoreFoundation 0x9075ca18 CFRunLoopRunSpecific + 268
> 4 com.apple.Foundation 0x928f5664 -[NSRunLoop
> runMode:beforeDate:] + 172
> 5 com.apple.Foundation 0x928f559c -[NSRunLoop run] + 76
> 6 com.apple.WebKit 0x95665410 +[WebFileDatabase
> _syncLoop:] + 176
> 7 com.apple.Foundation 0x928e66d4 forkThreadForFunction + 108
> 8 libSystem.B.dylib 0x9002b200 _pthread_body + 96
>
> Thread 0 crashed with PPC Thread State 64:
> srr0: 0x00000000067c42c0 srr1:
> 0x100000000200f030 vrsave: 0x0000000000000000
> cr: 0x42022448 xer: 0x0000000020000000 lr:
> 0x00000000067c41c0 ctr: 0x0000000000000000
> r0: 0x0000000000003840 r1: 0x00000000bfffc580 r2:
> 0x00000000075f9e98 r3: 0x0000000000000000
> r4: 0x00000000075f9858 r5: 0x00000000075f8598 r6:
> 0x00000000075f8bd8 r7: 0x00000000075f9218
> r8: 0x00000000fb3513df r9: 0x0000000006a5da58 r10:
> 0x00000000000000c7 r11: 0x0000000001bbf458
> r12: 0x00000000075f9858 r13: 0x0000000000000640 r14:
> 0x0000000001f9d018 r15: 0x0000000001b8f100
> r16: 0x0000000006a5d418 r17: 0x0000000000000002 r18:
> 0x0000000001bbee18 r19: 0x0000000006857d40
> r20: 0x00000000075f6018 r21: 0x00000000000000c8 r22:
> 0x0000000000002580 r23: 0x0000000000003840
> r24: 0x00000000000000c8 r25: 0x00000000000000c7 r26:
> 0x0000000000000640 r27: 0x0000000001bbee18
> r28: 0x0000000001f9d978 r29: 0x0000000000000037 r30:
> 0x00000000075f9218 r31: 0x00000000067c3bf0
>
> Binary Images Description:
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> R.app/Contents/MacOS/R
> 0x55000 - 0x87fff libreadline.5.0.dylib /Library/Frameworks/
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> 0x95fdb000 - 0x95fddfff com.apple.ExceptionHandling 1.2 (???) /System/
> Library/Frameworks/ExceptionHandling.framework/Versions/A/
> ExceptionHandling
> 0x96fba000 - 0x96fd9fff com.apple.vecLib 3.1.1 (vecLib 3.1.1) /System/
> Library/Frameworks/vecLib.framework/Versions/A/vecLib
>
> Model: PowerMac7,2, BootROM 5.0.7f0, 2 processors, PowerPC 970
> (2.2), 2 GHz, 8 GB
> Graphics: ATI Radeon 9600 Pro, ATY,RV350, AGP, 64 MB
> Memory Module: DIMM0/J11, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM1/J12, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM2/J13, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM3/J14, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM4/J41, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM5/J42, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM6/J43, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM7/J44, 1 GB, DDR SDRAM, PC3200U-30330
> Modem: MicroDash, UCJ, V.92, 1.0F, APPLE VERSION 2.6.6
> Network Service: Built-in Ethernet, Ethernet, en0
> Serial ATA Device: ST3160023AS, 149.05 GB
> Parallel ATA Device: PIONEER DVD-RW DVR-106D,
> USB Device: Flash Disk, USB, Up to 480 Mb/sec, 500 mA
> USB Device: hp LaserJet 1300, Hewlett-Packard, Up to 12 Mb/sec, 500 mA
> USB Device: Hub, , Up to 12 Mb/sec, 500 mA
> USB Device: Hub in Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/
> sec, 500 mA
> USB Device: Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec,
> 250 mA
> USB Device: Studio Display, , Up to 1.5 Mb/sec, 500 mA
> USB Device: Apple Optical USB Mouse, Logitech, Up to 1.5 Mb/sec, 500 mA
>
>
> ###########################
> ###OLD from Hmisc crash:
> I keep getting a "segmentation fault" when trying to run areg.boot in
> the Hmisc package. I include below output from two different attempts.
> Thank you in advance for any help.
>
> Hank Stevens
>
> The following is taken from the example in the areg.boot
> documentation, run inside Aquamacs Emacs:
>
> > set.seed(171) # to be able to reproduce example
> > x1 <- rnorm(200)
> > x2 <- runif(200) # a variable that is really unrelated to y]
> > x3 <- factor(sample(c('cat','dog','cow'), 200,TRUE)) # also
> unrelated to y
> > y <- exp(x1 + rnorm(200)/3)
> > f <- areg.boot(y ~ x1 + x2 + x3, B=40)
> Loading required package: acepack
>
> Process R segmentation fault at Thu Feb 16 14:13:44 2006
>
> ############
> The following is the automated report following the crash from the
> same code in the R GUI:
>
> Date/Time: 2006-02-16 14:18:21.336 -0500
> OS Version: 10.4.4 (Build 8G32)
> Report Version: 3
>
> Command: R
> Path: /Applications/R.app/Contents/MacOS/R
> Parent: WindowServer [75]
>
> Version: 1.14 (2129)
>
> PID: 902
> Thread: 0
>
> Exception: EXC_BAD_ACCESS (0x0001)
> Codes: KERN_INVALID_ADDRESS (0x0001) at 0x63110304
>
> Thread 0 Crashed:
> 0 acepack.so 0x0169a2c0 avas_ + 1752 (avas.f:112)
> 1 libR.dylib 0x0024f498 do_dotCode + 1844 (dotcode.c:
> 1722)
> 2 libR.dylib 0x00265cb0 Rf_eval + 1544 (eval.c:405)
> 3 libR.dylib 0x00267ccc do_set + 224 (eval.c:1309)
> 4 libR.dylib 0x00265af4 Rf_eval + 1100 (eval.c:382)
> 5 libR.dylib 0x0026744c do_begin + 136 (eval.c:1058)
> 6 libR.dylib 0x00265af4 Rf_eval + 1100 (eval.c:382)
> 7 libR.dylib 0x00266150 Rf_applyClosure + 952
> (eval.c:576)
> 8 libR.dylib 0x00265d2c Rf_eval + 1668 (eval.c:417)
> 9 libR.dylib 0x00268678 do_eval + 700 (eval.c:1568)
> 10 libR.dylib 0x0029acec do_internal + 392 (names.c:
> 1084)
> 11 libR.dylib 0x00265af4 Rf_eval + 1100 (eval.c:382)
> 12 libR.dylib 0x00266150 Rf_applyClosure + 952
> (eval.c:576)
> 13 libR.dylib 0x00265d2c Rf_eval + 1668 (eval.c:417)
> 14 libR.dylib 0x00267ccc do_set + 224 (eval.c:1309)
> 15 libR.dylib 0x00265af4 Rf_eval + 1100 (eval.c:382)
> 16 libR.dylib 0x0026744c do_begin + 136 (eval.c:1058)
> 17 libR.dylib 0x00265af4 Rf_eval + 1100 (eval.c:382)
> 18 libR.dylib 0x00266150 Rf_applyClosure + 952
> (eval.c:576)
> 19 libR.dylib 0x00265d2c Rf_eval + 1668 (eval.c:417)
> 20 libR.dylib 0x00267ccc do_set + 224 (eval.c:1309)
> 21 libR.dylib 0x00265af4 Rf_eval + 1100 (eval.c:382)
> 22 org.R-project.R 0x00015884 RGUI_ReplIteration + 500
> (crt.c:300)
> 23 org.R-project.R 0x00015674 RGUI_ReplConsole + 148
> (crt.c:300)
> 24 org.R-project.R 0x000155c8 run_REngineRmainloop + 156
> (crt.c:300)
> 25 org.R-project.R 0x0000e56c -[REngine runREPL] + 76
> (crt.c:300)
> 26 com.apple.Foundation 0x928e949c __NSFireTimer + 116
> 27 com.apple.CoreFoundation 0x90770aec __CFRunLoopDoTimer + 184
> 28 com.apple.CoreFoundation 0x9075d464 __CFRunLoopRun + 1680
> 29 com.apple.CoreFoundation 0x9075ca18 CFRunLoopRunSpecific + 268
> 30 com.apple.HIToolbox 0x9318e1e0 RunCurrentEventLoopInMode + 264
> 31 com.apple.HIToolbox 0x9318d874 ReceiveNextEventCommon + 380
> 32 com.apple.HIToolbox 0x9318d6e0
> BlockUntilNextEventMatchingListInMode + 96
> 33 com.apple.AppKit 0x9368b104 _DPSNextEvent + 384
> 34 com.apple.AppKit 0x9368adc8 -[NSApplication
> nextEventMatchingMask:untilDate:inMode:dequeue:] + 116
> 35 com.apple.AppKit 0x9368730c -[NSApplication run] + 472
> 36 com.apple.AppKit 0x93777e68 NSApplicationMain + 452
> 37 org.R-project.R 0x00002eb0 _start + 392 (crt.c:267)
> 38 dyld 0x8fe01048 _dyld_start + 60
>
> Thread 1:
> 0 libSystem.B.dylib 0x9001f20c select + 12
> 1 org.R-project.R 0x00004674 -[RController readThread:] +
> 524 (crt.c:300)
> 2 com.apple.Foundation 0x928e66d4 forkThreadForFunction + 108
> 3 libSystem.B.dylib 0x9002b200 _pthread_body + 96
>
> Thread 2:
> 0 libSystem.B.dylib 0x90049748 syscall_thread_switch + 8
> 1 com.apple.Foundation 0x928fead0 +[NSThread sleepUntilDate:]
> + 152
> 2 com.apple.AppKit 0x93728034 -[NSUIHeartBeat
> _heartBeatThread:] + 1100
> 3 com.apple.Foundation 0x928e66d4 forkThreadForFunction + 108
> 4 libSystem.B.dylib 0x9002b200 _pthread_body + 96
>
> Thread 0 crashed with PPC Thread State 64:
> srr0: 0x000000000169a2c0 srr1:
> 0x100000000200f030 vrsave: 0x0000000000000000
> cr: 0x48022448 xer: 0x0000000020000000 lr:
> 0x000000000169a1c0 ctr: 0x0000000000000000
> r0: 0x0000000000003840 r1: 0x00000000bfffa390 r2:
> 0x0000000006dd4e98 r3: 0x0000000000000000
> r4: 0x0000000006dd4858 r5: 0x0000000006dd3598 r6:
> 0x0000000006dd3bd8 r7: 0x0000000006dd4218
> r8: 0x0000000063110304 r9: 0x0000000007488658 r10:
> 0x00000000000000c7 r11: 0x000000000748a258
> r12: 0x0000000006dd4858 r13: 0x0000000000000640 r14:
> 0x000000000748a418 r15: 0x00000000071ec9a8
> r16: 0x0000000007488018 r17: 0x0000000000000004 r18:
> 0x0000000007489c18 r19: 0x00000000019fc7c0
> r20: 0x0000000006dd1018 r21: 0x00000000000000c8 r22:
> 0x0000000000002580 r23: 0x0000000000003840
> r24: 0x00000000000000c8 r25: 0x00000000000000c7 r26:
> 0x0000000000000640 r27: 0x0000000007489c18
> r28: 0x000000000748b3b8 r29: 0x0000000000000098 r30:
> 0x0000000006dd4218 r31: 0x0000000001699bf0
>
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> 0x9420a000 - 0x9420afff com.apple.audio.units.AudioUnit 1.4 /System/
> Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
> 0x9420c000 - 0x94384fff com.apple.QuartzCore 1.4.5 /System/Library/
> Frameworks/QuartzCore.framework/Versions/A/QuartzCore
> 0x943ce000 - 0x9440bfff libsqlite3.0.dylib /usr/lib/libsqlite3.0.dylib
> 0x94413000 - 0x94463fff libGLImage.dylib /System/Library/Frameworks/
> OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
> 0x94605000 - 0x94614fff libCGATS.A.dylib /System/Library/Frameworks/
> ApplicationServices.framework/Versions/A/Frameworks/
> CoreGraphics.framework/Versions/A/Resources/libCGATS.A.dylib
> 0x9461c000 - 0x94628fff libCSync.A.dylib /System/Library/Frameworks/
> ApplicationServices.framework/Versions/A/Frameworks/
> CoreGraphics.framework/Versions/A/Resources/libCSync.A.dylib
> 0x9466e000 - 0x94686fff libRIP.A.dylib /System/Library/Frameworks/
> ApplicationServices.framework/Versions/A/Frameworks/
> CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib
> 0x95663000 - 0x956effff com.apple.WebKit 417.9 /System/Library/
> Frameworks/WebKit.framework/Versions/A/WebKit
> 0x9574a000 - 0x9583ffff com.apple.JavaScriptCore 1.2 (417.8) /System/
> Library/Frameworks/WebKit.framework/Versions/A/Frameworks/
> JavaScriptCore.framework/Versions/A/JavaScriptCore
> 0x9587b000 - 0x95b85fff com.apple.WebCore 417.17 /System/Library/
> Frameworks/WebKit.framework/Versions/A/Frameworks/WebCore.framework/
> Versions/A/WebCore
> 0x95d0c000 - 0x95d35fff libxslt.1.dylib /usr/lib/libxslt.1.dylib
> 0x95fdb000 - 0x95fddfff com.apple.ExceptionHandling 1.2 (???) /System/
> Library/Frameworks/ExceptionHandling.framework/Versions/A/
> ExceptionHandling
> 0x96fba000 - 0x96fd9fff com.apple.vecLib 3.1.1 (vecLib 3.1.1) /System/
> Library/Frameworks/vecLib.framework/Versions/A/vecLib
>
> Model: PowerMac7,2, BootROM 5.0.7f0, 2 processors, PowerPC 970
> (2.2), 2 GHz, 8 GB
> Graphics: ATI Radeon 9600 Pro, ATY,RV350, AGP, 64 MB
> Memory Module: DIMM0/J11, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM1/J12, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM2/J13, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM3/J14, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM4/J41, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM5/J42, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM6/J43, 1 GB, DDR SDRAM, PC3200U-30330
> Memory Module: DIMM7/J44, 1 GB, DDR SDRAM, PC3200U-30330
> Modem: MicroDash, UCJ, V.92, 1.0F, APPLE VERSION 2.6.6
> Network Service: Built-in Ethernet, Ethernet, en0
> Serial ATA Device: ST3160023AS, 149.05 GB
> Parallel ATA Device: PIONEER DVD-RW DVR-106D,
> USB Device: Flash Disk, USB, Up to 480 Mb/sec, 500 mA
> USB Device: hp LaserJet 1300, Hewlett-Packard, Up to 12 Mb/sec, 500 mA
> USB Device: Hub, , Up to 12 Mb/sec, 500 mA
> USB Device: Hub in Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/
> sec, 500 mA
> USB Device: Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec,
> 250 mA
> USB Device: Studio Display, , Up to 1.5 Mb/sec, 500 mA
> USB Device: Apple Optical USB Mouse, Logitech, Up to 1.5 Mb/sec, 500 mA
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

______________________________________________
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Received on Fri Feb 17 09:17:46 2006

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