[R] segmentation fault with Hmisc areg.boot()

From: Martin Henry H. Stevens <HStevens_at_muohio.edu>
Date: Fri 17 Feb 2006 - 06:21:53 EST


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 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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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

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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Feb 17 06:25:35 2006

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