segmentation fault with Hmisc areg.boot()

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segmentation fault with Hmisc areg.boot()

Hank Stevens
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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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  
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Memory Module: DIMM3/J14, 1 GB, DDR SDRAM, PC3200U-30330
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Re: segmentation fault with Hmisc areg.boot()

Frank Harrell
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 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)

Works fine on debian linux with same versions

Frank

P.S.  In future it's best to omit prompts from lines of code for easy
pasting into the R prompt.

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Frank Harrell
Department of Biostatistics, Vanderbilt University
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Re: segmentation fault with Hmisc areg.boot()

PaulJohnson32gmail
On 2/16/06, Frank E Harrell Jr <[hidden email]> wrote:

> >
> > 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)
>
> Works fine on debian linux with same versions
>
> Frank


Works fine in Fedora Core 4 with R -2.2

in case more tests help to point finger at problematic OS

Paul Johnson


--
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

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