[R-sig-ME] lmer in R-devel suddenly failing using code that worked just a few days ago

[Mark W Kimpel]

Doug,

When I went to make a self-contained example, it worked. When I went 
back to my original code, it too worked. Only difference was restarting 
R. Wonder if there was a conflict with another package???

Solved for now at least, sorry for bothering the list,

Mark

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 204-4202 Home (no voice mail please)

mwkimpel<at>gmail<dot>com

******************************************************************


Douglas Bates wrote:
> On Thu, Mar 20, 2008 at 12:57 PM, Mark W Kimpel <mwkimpel at gmail.com> wrote:
>> lmer is producing an error using code that was working for me just a few
>>  days ago. Output and sessionInfo() follows. Note that the warning
>>  message has always been present. Thanks, Mark
>>
>>   >           Treatment <- factor(pData(AOP$eSet)$Treatment)
>>   >           Tissue <- factor(pData(AOP$eSet)$Tissue)
>>   >           Rat <- factor(pData(AOP$eSet)$Rat)
>>   >           Tissue <- factor(pData(AOP$eSet)$Tissue)
>>   >           mod1 <- lmer(gene.mat[1,] ~  Treatment + Tissue + (1|Rat))
>>  Warning message:
>>  In .local(x, ..., value) :
>>    Estimated variance for factor 'Rat' is effectively zero
>>
>>   > mod1
>>  Error in printMer(object) :
>>    no slot of name "status" for this object of class "table"
> 
> I don't think we can debug this without a reproducible example, Mark.
> The message indicates that inside printMer an object that should be of
> class summary.mer is of class "table".  My guess is that this occurs
> right at the beginning of that function
> 
> printMer <- function(x, digits = max(3, getOption("digits") - 3),
>                      correlation = TRUE, symbolic.cor = FALSE,
>                      signif.stars = getOption("show.signif.stars"), ...)
> {
>     so <- summary(x)
>     REML <- so at status["REML"]
> 
> during that first access to the status slot, but without a
> reproducible example we can't decide what has gone wrong getting to
> that point.
> 
> 
>>  Enter a frame number, or 0 to exit
>>
>>  1: function (object)
>>  2: function (object)
>>  3: printMer(object)
>>
>>  Selection: c
>>  Enter an item from the menu, or 0 to exit
>>  Selection: 0
>>   > sessionInfo()
>>  R version 2.7.0 Under development (unstable) (2008-03-05 r44683)
>>  x86_64-unknown-linux-gnu
>>
>>  locale:
>>  LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>>  attached base packages:
>>  [1] splines   tools     stats     graphics  grDevices datasets  utils
>>  [8] methods   base
>>
>>  other attached packages:
>>   [1] lme4_0.99875-9       Matrix_0.999375-5    lattice_0.17-6
>>   [4] affycoretools_1.11.4 annaffy_1.11.5       KEGG.db_2.1.3
>>   [7] gcrma_2.11.4         matchprobes_1.11.1   biomaRt_1.13.9
>>  [10] RCurl_0.8-3          GOstats_2.5.2        Category_2.5.7
>>  [13] genefilter_1.17.12   survival_2.34        RBGL_1.15.7
>>  [16] annotate_1.17.11     xtable_1.5-2         GO.db_2.1.3
>>  [19] AnnotationDbi_1.1.26 RSQLite_0.6-8        DBI_0.2-4
>>  [22] graph_1.17.17        limma_2.13.6         affy_1.17.9
>>  [25] preprocessCore_1.1.5 affyio_1.7.17        Biobase_1.99.3
>>
>>  loaded via a namespace (and not attached):
>>  [1] cluster_1.11.10 grid_2.7.0      XML_1.93-2
>>  --
>>
>>  Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
>>  Indiana University School of Medicine
>>
>>  15032 Hunter Court, Westfield, IN  46074
>>
>>  (317) 490-5129 Work, & Mobile & VoiceMail
>>  (317) 204-4202 Home (no voice mail please)
>>
>>  mwkimpel<at>gmail<dot>com
>>
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>>
>