[R-SIG-Mac] lme4 crashes R
John Maindonald
john.maindonald at anu.edu.au
Thu Aug 5 13:31:01 CEST 2004
Hi Andrew -
I had a problem when I tried to run it, also. It seems likely to me that
some modification is required to the code so that the compiler will
do the right thing.
John Maindonald.
> library(DAAG)
> library(lme4)
> tinting$id <- factor(tinting$id)
> tinting.lme <- lme(log(it) ~ sex+tint+target+agegp, random=~1|id,
+ data=tinting)
> print(tinting.lme)
Linear mixed-effects model fit by Data: NULL
Log-likelihood: NULL
Fixed: list()
NULL
Length Class Mode
0 NULL NULL
Number of Observations:
Number of Groups: Error in 1:dd$Q : NA/NaN argument
> summary(tinting.lme)
Process R bus error at Thu Jul 22 10:41:31 2004
--please do not edit the information below--
Version:
platform = powerpc-apple-darwin6.8
arch = powerpc
os = darwin6.8
system = powerpc, darwin6.8
status =
major = 1
minor = 9.1
year = 2004
month = 06
day = 21
language = R
Search Path:
.GlobalEnv, package:DAAG, package:lme4, package:Matrix,
package:methods, package:stats, package:graphics, package:utils,
Autoloads, package:base
On 5 Aug 2004, at 8:55 PM, Andrew Beckerman wrote:
> Hi -
>
> has anyone had success at building and running the source distribution
> of lme4 from CRAN on OSX? I find that it builds, and will load as a
> library, but running the lme example in lme4 causes R to crash - the
> data file loads, the model appears to run, but attempting a summary()
> or print() causes the crash. I notice that there is a binary of an
> old version of lme4, but nothing up to date.
>
> Running R in X-windows fails as well, producing a Bus Error.
>
> OSX 10.3.4, R1.9.1, Dev Tools installed, g77 from HPC;
> lme4_0.6-4.tar.gz.; Matrix version 0.8-10
>
> Below is the R.bin.crash.log file.
>
> Cheers
> andrew
>
> **********
>
> Host Name: dyn094076.shef.ac.uk
> Date/Time: 2004-08-05 11:28:33 +0100
> OS Version: 10.3.4 (Build 7H63)
> Report Version: 2
>
> Command: R.bin
> Path: /Library/Frameworks/R.framework/Resources/bin/R.bin
> Version: 1.9.1 (R 1.9.1)
> PID: 6947
> Thread: 0
>
> Exception: EXC_BAD_ACCESS (0x0001)
> Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x00000000
>
> Thread 0 Crashed:
> 0 R.bin 0x000ecef0 Rf_isVectorAtomic + 0 (util.c:340)
> 1 R.bin 0x000ec578 Rf_asLogical + 0x28 (util.c:93)
> 2 Matrix.so 0x06511414 ssclme_sigma + 0xb0 (ssclme.c:884)
> 3 R.bin 0x00045024 do_dotcall + 0x2f0 (dotcode.c:521)
> 4 R.bin 0x0005da10 Rf_eval + 0x5d8 (eval.c:398)
> 5 R.bin 0x0005f944 do_set + 0xe0 (eval.c:1287)
> 6 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 7 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 8 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 9 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 10 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 11 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 12 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 13 R.bin 0x0005e0cc R_execClosure + 0x1fc (eval.c:651)
> 14 R.bin 0x0005e3e8 R_execMethod + 0x2c4 (eval.c:753)
> 15 methods.so 0x0535bef8 R_standardGeneric + 0x298
> (methods_list_dispatch.c:610)
> 16 R.bin 0x00092fa0 do_standardGeneric + 0xcc (objects.c:982)
> 17 R.bin 0x0005da10 Rf_eval + 0x5d8 (eval.c:398)
> 18 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 19 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 20 R.bin 0x0005d724 Rf_eval + 0x2ec (eval.c:355)
> 21 R.bin 0x0005d684 Rf_eval + 0x24c (eval.c:342)
> 22 R.bin 0x0005d724 Rf_eval + 0x2ec (eval.c:355)
> 23 R.bin 0x0005d684 Rf_eval + 0x24c (eval.c:342)
> 24 R.bin 0x0005fbf4 Rf_evalList + 0x128 (eval.c:1360)
> 25 R.bin 0x0005d984 Rf_eval + 0x54c (eval.c:396)
> 26 R.bin 0x00060698 Rf_DispatchOrEval + 0x118 (eval.c:1664)
> 27 R.bin 0x000e7ad8 do_subset2 + 0x48 (subset.c:681)
> 28 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 29 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 30 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 31 R.bin 0x0005f944 do_set + 0xe0 (eval.c:1287)
> 32 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 33 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 34 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 35 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 36 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 37 R.bin 0x0005d724 Rf_eval + 0x2ec (eval.c:355)
> 38 R.bin 0x0005d684 Rf_eval + 0x24c (eval.c:342)
> 39 R.bin 0x0005d724 Rf_eval + 0x2ec (eval.c:355)
> 40 R.bin 0x0005d684 Rf_eval + 0x24c (eval.c:342)
> 41 R.bin 0x0005fbf4 Rf_evalList + 0x128 (eval.c:1360)
> 42 R.bin 0x0005d984 Rf_eval + 0x54c (eval.c:396)
> 43 R.bin 0x00060698 Rf_DispatchOrEval + 0x118 (eval.c:1664)
> 44 R.bin 0x000e7ad8 do_subset2 + 0x48 (subset.c:681)
> 45 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 46 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 47 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 48 R.bin 0x0005f944 do_set + 0xe0 (eval.c:1287)
> 49 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 50 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 51 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 52 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 53 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 54 R.bin 0x0005f944 do_set + 0xe0 (eval.c:1287)
> 55 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 56 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 57 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 58 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 59 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 60 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 61 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 62 R.bin 0x0005e0cc R_execClosure + 0x1fc (eval.c:651)
> 63 R.bin 0x0005e3e8 R_execMethod + 0x2c4 (eval.c:753)
> 64 methods.so 0x0535bef8 R_standardGeneric + 0x298
> (methods_list_dispatch.c:610)
> 65 R.bin 0x00092fa0 do_standardGeneric + 0xcc (objects.c:982)
> 66 R.bin 0x0005da10 Rf_eval + 0x5d8 (eval.c:398)
> 67 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 68 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 69 R.bin 0x0005d724 Rf_eval + 0x2ec (eval.c:355)
> 70 R.bin 0x0005d724 Rf_eval + 0x2ec (eval.c:355)
> 71 R.bin 0x0005fb84 Rf_evalList + 0xb8 (eval.c:1350)
> 72 R.bin 0x0005d984 Rf_eval + 0x54c (eval.c:396)
> 73 R.bin 0x0005f944 do_set + 0xe0 (eval.c:1287)
> 74 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 75 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 76 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 77 R.bin 0x0005e0cc R_execClosure + 0x1fc (eval.c:651)
> 78 R.bin 0x0005e3e8 R_execMethod + 0x2c4 (eval.c:753)
> 79 methods.so 0x0535bef8 R_standardGeneric + 0x298
> (methods_list_dispatch.c:610)
> 80 R.bin 0x00092fa0 do_standardGeneric + 0xcc (objects.c:982)
> 81 R.bin 0x0005da10 Rf_eval + 0x5d8 (eval.c:398)
> 82 R.bin 0x0005f944 do_set + 0xe0 (eval.c:1287)
> 83 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 84 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 85 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 86 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 87 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 88 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 89 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 90 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 91 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 92 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 93 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 94 R.bin 0x0005e0cc R_execClosure + 0x1fc (eval.c:651)
> 95 R.bin 0x0005e3e8 R_execMethod + 0x2c4 (eval.c:753)
> 96 methods.so 0x0535bef8 R_standardGeneric + 0x298
> (methods_list_dispatch.c:610)
> 97 R.bin 0x00092fa0 do_standardGeneric + 0xcc (objects.c:982)
> 98 R.bin 0x0005da10 Rf_eval + 0x5d8 (eval.c:398)
> 99 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 100 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 101 R.bin 0x0005f944 do_set + 0xe0 (eval.c:1287)
> 102 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 103 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 104 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 105 R.bin 0x0005e0cc R_execClosure + 0x1fc (eval.c:651)
> 106 R.bin 0x0005e3e8 R_execMethod + 0x2c4 (eval.c:753)
> 107 methods.so 0x0535bef8 R_standardGeneric + 0x298
> (methods_list_dispatch.c:610)
> 108 R.bin 0x00092fa0 do_standardGeneric + 0xcc (objects.c:982)
> 109 R.bin 0x0005da10 Rf_eval + 0x5d8 (eval.c:398)
> 110 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 111 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 112 R.bin 0x000bf4ac do_printdefault + 0x2a0 (print.c:220)
> 113 R.bin 0x000907e4 do_internal + 0x170 (names.c:1057)
> 114 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 115 R.bin 0x0005f12c do_begin + 0x88 (eval.c:1047)
> 116 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 117 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 118 R.bin 0x00090c78 applyMethod + 0x1d8 (objects.c:119)
> 119 R.bin 0x00091514 Rf_usemethod + 0x5b4 (objects.c:326)
> 120 R.bin 0x00091754 do_usemethod + 0x1f4 (objects.c:389)
> 121 R.bin 0x0005d85c Rf_eval + 0x424 (eval.c:375)
> 122 R.bin 0x0005de78 Rf_applyClosure + 0x390 (eval.c:566)
> 123 R.bin 0x0005da88 Rf_eval + 0x650 (eval.c:410)
> 124 R.bin 0x000c09a4 Rf_PrintValueEnv + 0x7c (print.c:776)
> 125 R.bin 0x00082a60 Rf_ReplIteration + 0x1f8 (main.c:255)
> 126 R.bin 0x00082b80 R_ReplConsole + 0x88 (main.c:299)
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> PPC Thread State:
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> 0x92d30000 - 0x92d80fff com.apple.HIServices 1.4.1
> (0.0.1d1) /System/Library/Frameworks/ApplicationServices.framework/
> Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
> 0x935d0000 - 0x938a8fff com.apple.CoreGraphics 1.203.20
> (???) /System/Library/Frameworks/ApplicationServices.framework/
> Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
> 0x939a0000 - 0x939b4fff libcups.2.dylib /usr/lib/libcups.2.dylib
> 0x939d0000 - 0x939d4fff libmathCommon.A.dylib
> /usr/lib/system/libmathCommon.A.dylib
> 0x94060000 - 0x94078fff com.apple.WebServices 1.1.1
> (1.1.0) /System/Library/Frameworks/CoreServices.framework/Versions/A/
> Frameworks/WebServicesCore.framework/Versions/A/WebServicesCore
> 0x94120000 - 0x9414bfff libncurses.5.dylib /usr/lib/libncurses.5.dylib
> 0x945b0000 - 0x945b9fff libz.1.dylib /usr/lib/libz.1.dylib
> 0x94610000 - 0x9462afff libresolv.9.dylib /usr/lib/libresolv.9.dylib
> 0x94650000 - 0x946affff com.apple.SearchKit
> 1.0.2 /System/Library/Frameworks/CoreServices.framework/Versions/A/
> Frameworks/SearchKit.framework/Versions/A/SearchKit
> 0x94b20000 - 0x94badfff com.apple.ink.framework
> 55.8 /System/Library/Frameworks/Carbon.framework/Versions/A/
> Frameworks/Ink.framework/Versions/A/Ink
> 0x954c0000 - 0x95ac6fff libBLAS.dylib
> /System/Library/Frameworks/Accelerate.framework/Versions/A/
> Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> 0x95b20000 - 0x95df0fff libLAPACK.dylib
> /System/Library/Frameworks/Accelerate.framework/Versions/A/
> Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
> 0x95e40000 - 0x95eadfff libvDSP.dylib
> /System/Library/Frameworks/Accelerate.framework/Versions/A/
> Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
> 0x95f00000 - 0x95f20fff libvMisc.dylib
> /System/Library/Frameworks/Accelerate.framework/Versions/A/
> Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
> 0x968d0000 - 0x969b2fff libicucore.A.dylib /usr/lib/libicucore.A.dylib
> 0x96a20000 - 0x96ae2fff libcrypto.0.9.7.dylib
> /usr/lib/libcrypto.0.9.7.dylib
> 0x96b40000 - 0x96b6efff libssl.0.9.7.dylib /usr/lib/libssl.0.9.7.dylib
> 0x96bf0000 - 0x96c7ffff ATS
> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/
> Frameworks/ATS.framework/Versions/A/ATS
> 0x96e80000 - 0x96e90fff com.apple.vecLib 3.0.1 (vecLib
> 3.0.1) /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
> 0x97510000 - 0x97518fff libbsm.dylib /usr/lib/libbsm.dylib
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac
>
>
John Maindonald email: john.maindonald at anu.edu.au
phone : +61 2 (6125)3473 fax : +61 2(6125)5549
Centre for Bioinformation Science, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
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