[R-sig-ME] Bug report for lme

Michal Figurski figurski at mail.med.upenn.edu
Mon Mar 14 14:34:03 CET 2011


It seems that I didn't make myself entirely clear, so here are a few 
clarifications. I also attach some data and a reproducible example that 
crashes R -  at least on my machine.

  - "hundreds of lines" - this was actually just one line in R output. 
This was part of the error message. I selected it and pasted into the 
email body, and it got converted to multiple lines... I agree this is 
unlikely to be helpful, though I was not sure, so I pasted the entire 
error message.
  - formula with 'paste()' is not a problem to me - I use it daily and 
it always works. Though for your convenience, in the attached code I 
used explicit formula - the outcome is unfortunately the same.
  - my .RData file is not corrupt and R starts normally. It only crashes 
after I run the problem code.

The code to reproduce the error:

# ******************************************************************* #
# Working example to reproduce crash

# Read the data in - replace path with your path
b      <- read.csv("crash-example.csv")
b$Aliq <- factor(b$Aliq)
b$SPL  <- factor(b$SPL)

# 1st example, to show that it works - on a selected set of data
# It takes a few moments, but it works - at least it doesn't crash R:
bb  <- b[b$SPL %in% unique(b$SPL[b$Plate=="TRT1"]),]
b.1 <- lmer(Conc~SPL + (SPL|Plate:Aliq)-1, data=bb)

# 2nd example - it takes only a few seconds and R crashes:
# R-version 2.12.2 on Win7 64bit
# Package lme4 version 0.999375-39
# Previously, when used in R 2.11.1 with lme4 version 0.999375-35,
# I got the error that I pasted in the message before, but the R
# did not crash.
b.2 <- lmer(Conc~SPL + (SPL|Plate:Aliq)-1, data=b)
# ******************************************************************* #

Kind regards,

Michal J. Figurski, PhD
HUP, Pathology & Laboratory Medicine
Biomarker Research Laboratory
3400 Spruce St. 7 Maloney S
Philadelphia, PA 19104
tel. (215) 662-3413

On 3/11/2011 4:00 PM, Douglas Bates wrote:
> On Fri, Mar 11, 2011 at 2:32 PM, Michal Figurski
> <figurski at mail.med.upenn.edu>  wrote:
>> Dear Prof. Bates,
>> I'm working with a lmer model using your lme4 library version 0.999375-35
>> with R 2.11.1 on Win7 64bit. Shortly after starting the function, the R
>> window clears and the following is being displayed:
>> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> ... Hundreds of lines deleted
>> REML = TRUE,  verbose = 0L)
>>   4: do.call(lmer_finalize, ans)
>>   5: lmer(formula(paste(i1, "~SPL + (SPL|Plate:Aliq)-1")), data = a)
>> Error in mer_finalize(ans) : caught access violation - continue with care
>> OK, so I updated R and lme4 to the latest versions, and now R just plainly
>> crashes without any message. Let me know if you need additional information
>> to troubleshoot.
> Well, hundreds, perhaps thousands, of lines of (part of)  a dump of an
> object are unlikely to be helpful.
> To get R working again you probably need to delete the file .RData in
> the default directory in which you start R.  It is most likely that
> you have a corrupt object in the saved worksheet.
> Secondly, using paste to create a formula is not a great idea.  The
> formula may have ended up being unevaluated.  If you really do need to
> use a character string to name the response variable the preferred
> approach is
> form<- substitute(foo ~ SPL + (SPL | Plate:Aliq) - 1, list(foo = as.name(i1)))
> lmer(form, data=a)
> If those suggestions don't help then please provide a reproducible
> example and preferrably on less than a gigantic data set.
> I am taking the liberty of cc:ing the R-SIG-Mixed-Models at R-project.org
> mailing list on this reply.  Many of those who read the list may be
> able to help you and it is unlikely I will be able to give much
> assistance soon because I am travelling for the next 10 days.
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