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

[Douglas Bates]

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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