[R-sig-ME] R crash for an lme4a example

Reinhold Kliegl reinhold.kliegl at gmail.com
Thu Apr 28 11:53:05 CEST 2011


This looks like the 32-bit problem again.  The example works fine on
MacBook Air with 64-bit R
Reinhold

> fm3.s <- lmer(Yield ~ 1|Batch, Dyestuff2, sparseX=TRUE)
>
> print(fm3.s)
Linear mixed model fit by REML ['merMod']
Formula: Yield ~ 1 | Batch
  Data: Dyestuff2
REML criterion at convergence: 161.8283

Random effects:
 Groups   Name        Variance Std.Dev.
 Batch    (Intercept)  0.00    0.000
 Residual             13.81    3.716
Number of obs: 30, groups: Batch, 6

Fixed effects:
           Estimate Std. Error t value
(Intercept)   5.6656     0.6784   8.352
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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

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

other attached packages:
[1] lme4a_0.999375-65  MatrixModels_0.2-1 minqa_1.1.15
Rcpp_0.9.4         Matrix_0.999375-50 lattice_0.19-23

loaded via a namespace (and not attached):
[1] codetools_0.2-8 grid_2.13.0     nlme_3.1-100    splines_2.13.0
stats4_2.13.0
On 28.04.2011, at 11:18, Ken Knoblauch wrote:


On Thu, Apr 28, 2011 at 11:18 AM, Ken Knoblauch <ken.knoblauch at inserm.fr> wrote:
> Hi,
>
> The following example from the lmer help page of lme4a causes R to crash
> on my system, copious crash report appended below the sessionInfo,
> just below.
>
> fm3.s <- lmer(Yield ~ 1|Batch, Dyestuff2, sparseX=TRUE)
>
> The other examples work without problem.
> It's version r1308 of lme4a, not indicated in the sessionInfo
> and it happened also with Rcpp 0.9.4, which I had tested first
> before upgrading to the latest version.
>
> Thanks.
>
> best,
>
> Ken
>
>> sessionInfo()
>
> R version 2.13.0 Patched (2011-04-20 r55568)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> [7] base
>
> other attached packages:
> [1] lme4a_0.999375-65  MatrixModels_0.2-1 minqa_1.1.15
> [4] Rcpp_0.9.4.1       Matrix_0.9996875-0 lattice_0.19-26
>
> loaded via a namespace (and not attached):
> [1] codetools_0.2-8 grid_2.13.0     nlme_3.1-100    splines_2.13.0
> [5] stats4_2.13.0   tools_2.13.0
>
>
> Process:         R [1972]
> Path:            /Applications/R.app/Contents/MacOS/R
> Identifier:      org.R-project.R
> Version:         R for Mac OS X GUI 1.40-devel Leopard build 32-bit (5761)
> Code Type:       X86 (Native)
> Parent Process:  launchd [65]
>
> Interval Since Last Report:          184 sec
> Crashes Since Last Report:           1
> Per-App Interval Since Last Report:  159 sec
> Per-App Crashes Since Last Report:   1
>
> Date/Time:       2011-04-28 11:09:15.815 +0200
> OS Version:      Mac OS X 10.5.8 (9L31a)
> Report Version:  6
> Anonymous UUID:  63A4D68C-0D99-4A8C-84B8-D9B452B18D7F
>
> Exception Type:  EXC_CRASH (SIGABRT)
> Exception Codes: 0x0000000000000000, 0x0000000000000000
> Crashed Thread:  0
>
> Thread 0 Crashed:
> 0   libSystem.B.dylib                   0x92671e42 __kill + 10
> 1   libSystem.B.dylib                   0x926e423a raise + 26
> 2   libSystem.B.dylib                   0x926f0679 abort + 73
> 3   libstdc++.6.dylib                   0x925a0005 0x92558000 + 294917
> 4   libstdc++.6.dylib                   0x9259e10c __gxx_personality_v0 +
> 1108
> 5   libstdc++.6.dylib                   0x9259e14b std::terminate() + 29
> 6   libstdc++.6.dylib                   0x9259e261 __cxa_throw + 101
> 7   minqa.so                            0x17f1572a
> Rcpp::Evaluator::run(SEXPREC*, SEXPREC*) + 378 (Evaluator.cpp:50)
> 8   minqa.so                            0x17f15834
> Rcpp::Evaluator::run(SEXPREC*) + 36 (Evaluator.cpp:59)
> 9   minqa.so                            0x17f15861
> Rcpp::internal::try_catch(SEXPREC*) + 17 (Evaluator.cpp:80)
> 10  minqa.so                            0x17f05186 calfun_ + 502
> (minqa.cpp:32)
> 11  minqa.so                            0x17f0ad9e prelim + 910
> (prelim.f:90)
> 12  minqa.so                            0x17f01041 bobyqb + 273
> (bobyqb.f:66)
> 13  minqa.so                            0x17f00e8d bobyqa + 749
> (bobyqa.f:143)
> 14  minqa.so                            0x17f06dfa bobyqa_cpp + 1034
> (minqa.cpp:93)
> 15  libR.dylib                          0x003f1971 do_dotcall + 1009
> (dotcode.c:856)
> 16  libR.dylib                          0x0041d181 Rf_eval + 1777
> (eval.c:508)
> 17  libR.dylib                          0x004202f6 do_set + 678
> (eval.c:1722)
> 18  libR.dylib                          0x0041cf82 Rf_eval + 1266
> (eval.c:482)
> 19  libR.dylib                          0x0041ec57 do_begin + 327
> (eval.c:1420)
> 20  libR.dylib                          0x0041cf82 Rf_eval + 1266
> (eval.c:482)
> 21  libR.dylib                          0x00421fc1 Rf_applyClosure + 833
> (eval.c:838)
> 22  libR.dylib                          0x0041ce82 Rf_eval + 1010
> (eval.c:526)
> 23  libR.dylib                          0x004202f6 do_set + 678
> (eval.c:1722)
> 24  libR.dylib                          0x0041cf82 Rf_eval + 1266
> (eval.c:482)
> 25  libR.dylib                          0x0041ec57 do_begin + 327
> (eval.c:1420)
> 26  libR.dylib                          0x0041cf82 Rf_eval + 1266
> (eval.c:482)
> 27  libR.dylib                          0x0041cf82 Rf_eval + 1266
> (eval.c:482)
> 28  libR.dylib                          0x0041ec57 do_begin + 327
> (eval.c:1420)
> 29  libR.dylib                          0x0041cf82 Rf_eval + 1266
> (eval.c:482)
> 30  libR.dylib                          0x00421fc1 Rf_applyClosure + 833
> (eval.c:838)
> 31  libR.dylib                          0x0041ce82 Rf_eval + 1010
> (eval.c:526)
> 32  libR.dylib                          0x004202f6 do_set + 678
> (eval.c:1722)
> 33  libR.dylib                          0x0041cf82 Rf_eval + 1266
> (eval.c:482)
> 34  libR.dylib                          0x00457651 R_ReplDLLdo1 + 513
> (main.c:360)
> 35  org.R-project.R                     0x0001fc5c run_REngineRmainloop +
> 252
> 36  org.R-project.R                     0x00014f2c -[REngine runREPL] + 284
> 37  org.R-project.R                     0x00003380 main + 1024
> 38  org.R-project.R                     0x00002dc6 start + 54
>
> Thread 1:
> 0   libSystem.B.dylib                   0x9260b44e __semwait_signal + 10
> 1   libSystem.B.dylib                   0x92635dcd
> pthread_cond_wait$UNIX2003 + 73
> 2   com.apple.JavaScriptCore            0x944107ff
> WTF::TCMalloc_PageHeap::scavengerThread() + 175
> 3   com.apple.JavaScriptCore            0x94410b1f
> WTF::TCMalloc_PageHeap::runScavengerThread(void*) + 15
> 4   libSystem.B.dylib                   0x92635155 _pthread_start + 321
> 5   libSystem.B.dylib                   0x92635012 thread_start + 34
>
> Thread 2:
> 0   libSystem.B.dylib                   0x92604266 mach_msg_trap + 10
> 1   libSystem.B.dylib                   0x9260ba5c mach_msg + 72
> 2   com.apple.CoreFoundation            0x901e4e7e CFRunLoopRunSpecific +
> 1790
> 3   com.apple.CoreFoundation            0x901e5aa8 CFRunLoopRunInMode + 88
> 4   com.apple.CFNetwork                 0x94b6918c
> CFURLCacheWorkerThread(void*) + 388
> 5   libSystem.B.dylib                   0x92635155 _pthread_start + 321
> 6   libSystem.B.dylib                   0x92635012 thread_start + 34
>
> Thread 3:
> 0   com.apple.CoreFoundation            0x902667a6 __CFDoExternRefOperation
> + 294
> 1   com.apple.CoreFoundation            0x902668da -[NSObject retain] + 26
> 2   com.apple.CoreFoundation            0x902636ab +[NSInvocation
> invocationWithMethodSignature:] + 59
> 3   com.apple.Foundation                0x94c9d915 -[NSDistantObject
> methodSignatureForSelector:] + 1173
> 4   com.apple.CoreFoundation            0x9026455d ___forwarding___ + 237
> 5   com.apple.CoreFoundation            0x902648b2 _CF_forwarding_prep_0 +
> 50
> 6   org.R-project.R                     0x00011c85 -[RController
> readThread:] + 2181
> 7   com.apple.Foundation                0x94c67dfd -[NSThread main] + 45
> 8   com.apple.Foundation                0x94c679a4 __NSThread__main__ + 308
> 9   libSystem.B.dylib                   0x92635155 _pthread_start + 321
> 10  libSystem.B.dylib                   0x92635012 thread_start + 34
>
> Thread 4:
> 0   libSystem.B.dylib                   0x9260b44e __semwait_signal + 10
> 1   libSystem.B.dylib                   0x9260b216 usleep$UNIX2003 + 61
> 2   com.apple.AppKit                    0x9035cbf1 -[NSUIHeartBeat
> _heartBeatThread:] + 2042
> 3   com.apple.Foundation                0x94c67dfd -[NSThread main] + 45
> 4   com.apple.Foundation                0x94c679a4 __NSThread__main__ + 308
> 5   libSystem.B.dylib                   0x92635155 _pthread_start + 321
> 6   libSystem.B.dylib                   0x92635012 thread_start + 34
>
> Thread 5:
> 0   libSystem.B.dylib                   0x9260b44e __semwait_signal + 10
> 1   libSystem.B.dylib                   0x92635dcd
> pthread_cond_wait$UNIX2003 + 73
> 2   com.apple.QuartzCore                0x97713a09 fe_fragment_thread + 54
> 3   libSystem.B.dylib                   0x92635155 _pthread_start + 321
> 4   libSystem.B.dylib                   0x92635012 thread_start + 34
>
> Thread 6:
> 0   libSystem.B.dylib                   0x92604266 mach_msg_trap + 10
> 1   libSystem.B.dylib                   0x9260ba5c mach_msg + 72
> 2   com.apple.CoreFoundation            0x901e4e7e CFRunLoopRunSpecific +
> 1790
> 3   com.apple.CoreFoundation            0x901e5aa8 CFRunLoopRunInMode + 88
> 4   com.apple.Foundation                0x94ccb520
> +[NSURLConnection(NSURLConnectionReallyInternal) _resourceLoadLoop:] + 320
> 5   com.apple.Foundation                0x94c67dfd -[NSThread main] + 45
> 6   com.apple.Foundation                0x94c679a4 __NSThread__main__ + 308
> 7   libSystem.B.dylib                   0x92635155 _pthread_start + 321
> 8   libSystem.B.dylib                   0x92635012 thread_start + 34
>
> Thread 7:
> 0   libSystem.B.dylib                   0x926536fa select$DARWIN_EXTSN + 10
> 1   libSystem.B.dylib                   0x92635155 _pthread_start + 321
> 2   libSystem.B.dylib                   0x92635012 thread_start + 34
>
> Thread 0 crashed with X86 Thread State (32-bit):
>  eax: 0x00000000  ebx: 0x926f0639  ecx: 0xbfffdbfc  edx: 0x92671e42
>  edi: 0xa039b5b8  esi: 0x19abc41c  ebp: 0xbfffdc18  esp: 0xbfffdbfc
>   ss: 0x0000001f  efl: 0x00000286  eip: 0x92671e42   cs: 0x00000007
>   ds: 0x0000001f   es: 0x0000001f   fs: 0x00000000   gs: 0x00000037
>  cr2: 0xffe2a3d0
>
> Binary Images:
>    0x1000 -    0x60ff7 +org.R-project.R R for Mac OS X GUI 1.40-devel
> Leopard build 32-bit (5761) <e4a59ae993daec6e4e40f98b2817aba3>
> /Applications/R.app/Contents/MacOS/R
>   0xa3000 -    0xa5fff  com.apple.ExceptionHandling 1.5 (10)
> /System/Library/Frameworks/ExceptionHandling.framework/Versions/A/ExceptionHandling
>   0xac000 -    0xd8fff +libRblas.dylib ??? (???)
> <f33c97123c677febd0a67f52f6dc0648>
> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libRblas.dylib
>   0xdd000 -   0x102ff3 +libreadline.5.2.dylib ??? (???)
> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib
>  0x374000 -   0x606fe3 +libR.dylib ??? (???)
> <fde27aeafc7c08100b2c0310fd8d7823>
> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib
>  0x6e8000 -   0x773fff +libgfortran.2.dylib ??? (???)
> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib
> 0x148be000 - 0x14ac6fef  com.apple.RawCamera.bundle 2.1.3 (537)
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> /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
> 0x16b22000 - 0x16b27ff3  libCGXCoreImage.A.dylib ??? (???)
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> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGXCoreImage.A.dylib
> 0x16b74000 - 0x16b79ffe +methods.so ??? (???)
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> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/methods/libs/i386/methods.so
> 0x16c7a000 - 0x16cd6fe7 +stats.so ??? (???)
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> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/stats/libs/i386/stats.so
> 0x16d94000 - 0x16dbdffa +grDevices.so ??? (???)
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> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/grDevices/libs/i386/grDevices.so
> 0x16fe4000 - 0x16fe7fff +lattice.so ??? (???)
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> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/lattice/libs/i386/lattice.so
> 0x16feb000 - 0x16fedff2 +splines.so ??? (???)
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> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/splines/libs/i386/splines.so
> 0x16ff4000 - 0x16ff7fff +tools.so ??? (???)
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> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/tools/libs/i386/tools.so
> 0x17863000 - 0x1786ffef +internet.so ??? (???)
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> /Library/Frameworks/R.framework/Resources/modules/i386/internet.so
> 0x178ae000 - 0x178c7fff +grid.so ??? (???)
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> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/grid/libs/i386/grid.so
> 0x179fa000 - 0x17a7efef +Matrix.so ??? (???)
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> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/Matrix/libs/i386/Matrix.so
> 0x17a9a000 - 0x17bdefe3 +libRlapack.dylib ??? (???)
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> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libRlapack.dylib
> 0x17c69000 - 0x17cf4fff +libgfortran.2.dylib ??? (???)
> /usr/local/lib/libgfortran.2.dylib
> 0x17e69000 - 0x17e70fed +libgcc_s.1.dylib ??? (???)
> /usr/local/lib/libgcc_s.1.dylib
> 0x17e93000 - 0x17ec3ff5 +Rcpp.so ??? (???)
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> /Users/knoblauch/Library/R/2.13/library/Rcpp/libs/i386/Rcpp.so
> 0x17efb000 - 0x17f1efff +minqa.so ??? (???)
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> /Users/knoblauch/Library/R/2.13/library/minqa/libs/i386/minqa.so
> 0x17f9b000 - 0x17fa7fff +nlme.so ??? (???)
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> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/nlme/libs/i386/nlme.so
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> /Users/knoblauch/Library/R/2.13/library/lme4a/libs/i386/lme4a.so
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> /usr/lib/dyld
> 0x90003000 - 0x90022ffa  libJPEG.dylib ??? (???)
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> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
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> /System/Library/PrivateFrameworks/CoreMediaIOServices.framework/Versions/A/CoreMediaIOServices
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> /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
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> /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
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> 0x97b7c000 - 0x97d4dfef  com.apple.security 5.0.7 (1)
> <44e26a9c40630a54d5a9f70c18483411>
> /System/Library/Frameworks/Security.framework/Versions/A/Security
> 0x97d4e000 - 0x97d4effc  com.apple.audio.units.AudioUnit 1.5 (1.5)
> /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
> 0x97d4f000 - 0x97d7eff7  libncurses.5.4.dylib ??? (???)
> <3b2ac2ca8190942b6b81d2a7012ea859> /usr/lib/libncurses.5.4.dylib
> 0x97d84000 - 0x97e01fef  libvMisc.dylib ??? (???)
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
> 0x97e02000 - 0x97e7cff8  com.apple.print.framework.PrintCore 5.5.4 (245.6)
> <03d0585059c20cb0bde5e000438c49e1>
> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
> 0xfffe8000 - 0xfffebfff  libobjc.A.dylib ??? (???) /usr/lib/libobjc.A.dylib
> 0xffff0000 - 0xffff1780  libSystem.B.dylib ??? (???)
> /usr/lib/libSystem.B.dylib
>
>
>
> --
> Ken Knoblauch
> Inserm U846
> Stem-cell and Brain Research Institute
> Department of Integrative Neurosciences
> 18 avenue du Doyen Lépine
> 69500 Bron
> France
> tel: +33 (0)4 72 91 34 77
> fax: +33 (0)4 72 91 34 61
> portable: +33 (0)6 84 10 64 10
> http://www.sbri.fr/members/kenneth-knoblauch.html
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>




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