Re: [R] Bug in lmer?

From: Renaud Lancelot <renaud.lancelot_at_gmail.com>
Date: Fri 30 Sep 2005 - 22:21:46 EST

I got a crash too with my Win XP config running:

platform i386-pc-mingw32

arch     i386
os       mingw32

system i386, mingw32
status beta
major 2
minor 2.0
year 2005
month 09
day 24
svn rev 35666
language R
Package:       Matrix
Version:       0.98-7
Date:          2005-09-09

Package:       lme4
Version:       0.98-1
Date:          2005-07-27

The monitoring of the crash with Dr.MingW provided the following information:

Rgui.exe caused an Access Violation at location 1001ed89 in module R.dll Writing to location 00000008.

Registers:

eax=00000000 ebx=00000040 ecx=011c8a18 edx=011c8058 esi=011c8a40 edi=00000018
eip=1001ed89 esp=0022dc20 ebp=0022dc48 iopl=0         nv up ei pl nz ac pe nc
cs=001b  ss=0023  ds=0023  es=0023  fs=003b  gs=0000             efl=00000212

Call stack:

1001ED89  R.dll:1001ED89  malloc_usable_size
1001FC2A  R.dll:1001FC2A  Rm_malloc
1009EF69  R.dll:1009EF69  Rf_allocVector
100389D8  R.dll:100389D8  do_makevector
100A6141  R.dll:100A6141  do_internal
10081FBF  R.dll:10081FBF  Rf_eval
10084C2B  R.dll:10084C2B  Rf_applyClosure
10081D50  R.dll:10081D50  Rf_eval
10084C2B  R.dll:10084C2B  Rf_applyClosure
10081D50  R.dll:10081D50  Rf_eval
10083985  R.dll:10083985  do_set
10081FBF  R.dll:10081FBF  Rf_eval
10083A55  R.dll:10083A55  do_begin
10081FBF  R.dll:10081FBF  Rf_eval
10084C2B  R.dll:10084C2B  Rf_applyClosure
10081D50  R.dll:10081D50  Rf_eval
10081FBF  R.dll:10081FBF  Rf_eval
10083985  R.dll:10083985  do_set
10081FBF  R.dll:10081FBF  Rf_eval
10083A55  R.dll:10083A55  do_begin
10081FBF  R.dll:10081FBF  Rf_eval
1008457D  R.dll:1008457D  do_if
1008489B  R.dll:1008489B  R_execMethod

016A2907 methods.dll:016A2907 R_standardGeneric
100A9254  R.dll:100A9254  do_standardGeneric
10082094  R.dll:10082094  Rf_eval
10084C2B  R.dll:10084C2B  Rf_applyClosure
10081D50  R.dll:10081D50  Rf_eval
10083985  R.dll:10083985  do_set
10081FBF  R.dll:10081FBF  Rf_eval
10083716  R.dll:10083716  Rf_DispatchOrEval
10081FBF  R.dll:10081FBF  Rf_eval
10083A55  R.dll:10083A55  do_begin
10081FBF  R.dll:10081FBF  Rf_eval
10081FBF  R.dll:10081FBF  Rf_eval
10083A55  R.dll:10083A55  do_begin
10081FBF  R.dll:10081FBF  Rf_eval
1008457D  R.dll:1008457D  do_if
1008489B  R.dll:1008489B  R_execMethod

016A2907 methods.dll:016A2907 R_standardGeneric
100A9254  R.dll:100A9254  do_standardGeneric
10082094  R.dll:10082094  Rf_eval
10084C2B  R.dll:10084C2B  Rf_applyClosure
10081D50  R.dll:10081D50  Rf_eval
10083985  R.dll:10083985  do_set
10081FBF  R.dll:10081FBF  Rf_eval
1009AAF5  R.dll:1009AAF5  Rf_ReplIteration
1009AC27  R.dll:1009AC27  Rf_ReplIteration
1009AEB7  R.dll:1009AEB7  run_Rmainloop
004013AA  Rgui.exe:004013AA
00401315  Rgui.exe:00401315
00401568  Rgui.exe:00401568

00401236 Rgui.exe:00401236
00401288 Rgui.exe:00401288
7C816D4F kernel32.dll:7C816D4F RegisterWaitForInputIdle

Best,

Renaud

2005/9/30, Martin Maechler <maechler@stat.math.ethz.ch>:
> >>>>> "Mark" == Mark Lyman <mlyman@byu.edu>
> >>>>> on Thu, 29 Sep 2005 14:44:38 -0600 writes:
>
> Mark> I am relatively new to R so I am not confident enough in what I am doing
> Mark> to be certain this is a bug.
>
>
> Mark> I am running R 2.1.1 on a Windows XP
> Mark> machine and the lme4 package version 0.98-1.
>
> lme4 nowadays is heavily based on "Matrix" which version are you
> using there?
>
> Mark> The following code fits the model I want using the
> Mark> nlme package version 3.1-60.
>
> < .............. > {see a script at the end}
>
> Mark> The problem is that when I try fitting the model using
> Mark> the lmer function with the following code:
>
> Mark> lmer(adg~trt+(1|loc)+(1|block:loc)+(1|loc:trt),mltloc)
>
> Mark> I get this message from Windows and R closes.
>
> Mark> >> R for Windows GUI front-end has encountered a problem and needs to
> Mark> >> close. We are sorry for the inconvenience.
>
> That definitely means there is a bug.
> The question is *where* the bug is: "lme4", "Matrix", "R", "Windows".
>
> One first thing coming to mind is a mismatch of "lme4" and "Matri
>
> Mark> This same code works on a Macintosh. So it doesn't
> Mark> seem that I have made an error in my code.
>
> correct; I can also fit the model nice and quickly on Linux,
> and summary() confirms the same fit {with the "usual problem" of
> different estimates for the degrees of freedoms 'df'}.
>
> So currently the bug only shows on the Windows platform.
> Could it be that you have a mismatching package "Matrix" version
> there, but not on the Mac?
>
> Mark> Also if anyone of the random effect terms is removed there is
> Mark> no problem. Is this something that is being looked at?
>
> not yet, AFAIK.
>
> Mark> Or I have I made a mistake somewhere? I have included
> Mark> the data that I am using below.
>
> I'm putting the data and an R script up for FTP,
> so that you or others can run this ``from anywhere'' via
>
> source("ftp://stat.ethz.ch/U/maechler/R/mltloc-ex.R", echo = TRUE)
>
> Maybe this helps diagnosis,
> Martin Maechler
>
> ______________________________________________
> 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
>



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 Received on Fri Sep 30 22:24:44 2005

This archive was generated by hypermail 2.1.8 : Sun 23 Oct 2005 - 18:05:07 EST