[R-sig-ME] possible lmer compatibility bug?

[Douglas Bates]

Thanks for sending the additional information.  There are two things
you can try immediately.

Don't simultaneously load the lme4 and the nlme packages.  It is
unfortunate that the packages conflict with each other but they do
because there are incompatible definitions of some of the extractor
functions.

Update your version of the lme4 package.  The version you are using is
quite out of date.   Just run

update.packages()

to get the updated versions.

On Wed, Aug 20, 2008 at 1:10 PM, Brandon Invergo
<brandon at brandoninvergo.com> wrote:
> Well, I'm not sure how to give you a reproducible example. What I can say is
> that it happens every time I use lmer() in R 2.7.1, for any model formula.
> Using the same data file, lmer() successfully completes in 2.7.0 but it
> returns the error in 2.7.1. For what it's worth, here's an example (in the
> data, dev.time is an integer, sex and temp are factors (2 levels and 5
> levels, resp.), and sleeve.in.temp is a random variable):
>
> 2.7.0:
>
>> dev.modelc <- lmer(dev.time ~ sex*temp + (1|sleeve.in.temp),
>> data=data.clean, family=Gamma(link="log"))
>> summary(dev.modelc)
> Generalized linear mixed model fit using Laplace
> Formula: dev.time ~ sex * temp + (1 | sleeve.in.temp)
>  Data: data.clean
> Family: Gamma(log link)
>  AIC   BIC logLik deviance
> 29.28 87.32 -3.639    7.277
> Random effects:
> Groups         Name        Variance   Std.Dev. sleeve.in.temp (Intercept)
> 2.5683e-12 1.6026e-06
> Residual                   5.1366e-03 7.1670e-02
> number of obs: 1446, groups: sleeve.in.temp, 54
>
> Fixed effects:
>            Estimate Std. Error t value
> (Intercept)  3.659500   0.005993   610.6
> sexm        -0.088450   0.008956    -9.9
> temp21      -0.207295   0.008132   -25.5
> temp23      -0.433156   0.008363   -51.8
> temp25      -0.612696   0.008491   -72.2
> temp27      -0.755628   0.008297   -91.1
> sexm:temp21  0.008189   0.012000     0.7
> sexm:temp23 -0.003357   0.012243    -0.3
> sexm:temp25 -0.014887   0.012321    -1.2
> sexm:temp27  0.010674   0.012405     0.9
>
> Correlation of Fixed Effects:
>           (Intr) sexm   temp21 temp23 temp25 temp27 sxm:21 sxm:23 sxm:25
> sexm        -0.669
> temp21      -0.737  0.493
>  temp23      -0.717  0.480  0.528
> temp25      -0.706  0.472  0.520  0.506
>  temp27      -0.722  0.483  0.532  0.518  0.510
> sexm:temp21  0.499 -0.746 -0.678 -0.358 -0.353 -0.361
>  sexm:temp23  0.490 -0.731 -0.361 -0.683 -0.346 -0.354  0.546
> sexm:temp25  0.486 -0.727 -0.358 -0.349 -0.689 -0.351  0.542  0.532
>  sexm:temp27  0.483 -0.722 -0.356 -0.346 -0.341 -0.669  0.539  0.528  0.525
>>sessionInfo()
> R version 2.7.0 (2008-04-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] gplots_2.6.0      gdata_2.4.2       gtools_2.5.0      nlme_3.1-88
> [5] lme4_0.99875-9    Matrix_0.999375-9 lattice_0.17-6
> loaded via a namespace (and not attached):
> [1] grid_2.7.0
>
>
>
>
> and for 2.7.1:
>> dev.modelc <- lmer(dev.time ~ sex*temp + (1|sleeve.in.temp),
>> data=data.clean, family=Gamma(link="log"))
>> summary(dev.modelc)
> Error in asMethod(object) : matrix is not symmetric [1,2]
>> traceback()
> 15: .Call(dense_to_symmetric, from, "U", TRUE)
> 14: asMethod(object)
> 13: as(from, "symmetricMatrix")
> 12: .class1(object)
> 11: as(as(from, "symmetricMatrix"), "dMatrix")
> 10: .class1(object)
> 9: as(as(as(from, "symmetricMatrix"), "dMatrix"), "denseMatrix")
> 8: .class1(object)
> 7: as(as(as(as(from, "symmetricMatrix"), "dMatrix"), "denseMatrix"),
>      "dpoMatrix")
> 6: asMethod(object)
> 5: as(sigma(object)^2 * chol2inv(object at RX, size = object at dims["p"]),
>      "dpoMatrix")
> 4: vcov(object)
> 3: vcov(object)
> 2: summary(dev.modelc)
> 1: summary(dev.modelc)
>> sessionInfo()
> R version 2.7.1 (2008-06-23)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] gplots_2.6.0       gdata_2.4.2        gtools_2.5.0       nlme_3.1-89
>  [5] lme4_0.999375-25   Matrix_0.999375-11 lattice_0.17-8
> loaded via a namespace (and not attached):
> [1] grid_2.7.1
>
>
> I'm sorry, I wasn't aware of the sessionInfo() or traceback() functions as
> this was the first time I've ever encountered an error like this in R. I'll
> be sure to be more courteous and include them next time...
>
>
>
>
>
>
>
> Douglas Bates wrote:
>>
>> On Wed, Aug 20, 2008 at 12:02 PM, Brandon Invergo
>> <brandon at brandoninvergo.com> wrote:
>>
>>>
>>> Dear all,
>>>
>>
>>
>>>
>>> I was just driving myself crazy trying to figure out this sudden error
>>> message I was getting on lines of code that were working fine the other
>>> day.
>>> Every time I tried to make a model with the lmer() function, it would
>>> return
>>> the following error: "Error in asMethod(object) : matrix is not symmetric
>>> [1,2]"
>>>
>>
>>
>>>
>>> I realized, though, that the only thing that had changed was the version
>>> of
>>> R I was using, having just switched to version 2.7.1. Sure enough, when I
>>> loaded up v2.7.0, the script worked fine and I could successfully call
>>> lmer.
>>>
>>
>>
>>>
>>> Is there something I'm possibly doing wrong that's preventing it from
>>> working in 2.7.1? Or is this a known problem?
>>>
>>
>> It appears that you have too high a regard for the readers of this
>> list in that you expect them to have psychic powers :-)
>>
>> More seriously, if you read your message and think of how a person
>> could possibly create a meaningful response based on the information
>> that you have given us, I think you will see that we don't have nearly
>> enough information to go on.
>>
>> A reproducible example rather than a description of "lines of code
>> that were working fine" is what we will need before we can expect to
>> provide a useful answer to you.  Also, information like the output
>> from
>>
>> sessionInfo()
>>
>> and perhaps
>>
>> traceback()
>>
>> after the error message so we know what was going on at the time the
>> error occurred.  Most importantly, we need to know what the call was
>> that resulted in an error.
>>
>
>