R Development Page

lme4a log file (check_x86_64_linux)

Fri Feb 15 13:39:31 2013: Checking package lme4a (SVN revision 1505) ...
* using log directory ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4a.Rcheck’
* using R version 2.15.2 Patched (2013-02-13 r61942)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘lme4a/DESCRIPTION’ ... OK
* this is package ‘lme4a’ version ‘0.9996875-1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘’
New submission
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking whether package ‘lme4a’ can be installed ... [98s/237s] OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... WARNING
Error: .onLoad failed in loadNamespace() for ‘lme4a’, details:
  call: value[[3L]](cond)
  error: failed to load module lme4 from package lme4a
could not find function "getClass"
In addition: Warning message:
No function found corresponding to methods exports from ‘MatrixModels’ for: ‘show’ 
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
anova.merMod: warning in pchisq(chisq, dfChisq, lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
anovaLmer: warning in pchisq(chisq, dfChisq, lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
bootMer: warning in matrix(t0, nr = length(t0), nc = nsim): partial
  argument match of 'nr' to 'nrow'
bootMer: warning in matrix(t0, nr = length(t0), nc = nsim): partial
  argument match of 'nc' to 'ncol'
formatVC: warning in matrix("", nr = nrow(reMat) - nrow(corr), nc =
  ncol(corr)): partial argument match of 'nr' to 'nrow'
formatVC: warning in matrix("", nr = nrow(reMat) - nrow(corr), nc =
  ncol(corr)): partial argument match of 'nc' to 'ncol'
mkReTrms : mkBlist: warning in matrix(seq_len(nc * nl), nc = nl, byrow
  = TRUE): partial argument match of 'nc' to 'ncol'
mkReTrms : : warning in matrix(seq_len(nb[i]), nc = nc[i],
  byrow = TRUE): partial argument match of 'nc' to 'ncol'
plot.lmList.confint: warning in gl(dd[3], dd[1] * dd[2], len = ll, lab
  = dn[[3]]): partial argument match of 'len' to 'length'
plot.lmList.confint: warning in gl(dd[3], dd[1] * dd[2], len = ll, lab
  = dn[[3]]): partial argument match of 'lab' to 'labels'
plot.lmList.confint: warning in gl(dd[2], dd[1], len = ll): partial
  argument match of 'len' to 'length'
print.merMod: warning in abbreviate(rn, minlen = 11): partial argument
  match of 'minlen' to 'minlength'
print.merMod: warning in matrix(format(round(corF@x, 3), nsmall = 3),
  nc = p, dimnames = list(rns, abbreviate(rn, minlen = 6))): partial
  argument match of 'nc' to 'ncol'
print.merMod: warning in abbreviate(rn, minlen = 6): partial argument
  match of 'minlen' to 'minlength'
print.summary.mer: warning in abbreviate(rn, minlen = 11): partial
  argument match of 'minlen' to 'minlength'
print.summary.mer: warning in matrix(format(round(corF@x, 3), nsmall =
  3), nc = p, dimnames = list(rns, abbreviate(rn, minlen = 6))):
  partial argument match of 'nc' to 'ncol'
print.summary.mer: warning in abbreviate(rn, minlen = 6): partial
  argument match of 'minlen' to 'minlength'
printMerenv: warning in abbreviate(rn, minlen = 11): partial argument
  match of 'minlen' to 'minlength'
printMerenv: warning in matrix(format(round(corF@x, 3), nsmall = 3), nc
  = p, dimnames = list(rns, abbreviate(rn, minlen = 6))): partial
  argument match of 'nc' to 'ncol'
printMerenv: warning in abbreviate(rn, minlen = 6): partial argument
  match of 'minlen' to 'minlength'
profile.merMod: warning in matrix(res, nr = maxpts, nc = length(res),
  dimnames = list(NULL, names(res)), byrow = TRUE): partial argument
  match of 'nr' to 'nrow'
profile.merMod: warning in matrix(res, nr = maxpts, nc = length(res),
  dimnames = list(NULL, names(res)), byrow = TRUE): partial argument
  match of 'nc' to 'ncol'
ranef.merMod: warning in matrix(ml[[i]], nc = nc[i], byrow = TRUE,
  dimnames = list(NULL, cnms[[i]])): partial argument match of 'nc' to
  'ncol'
simulate.merMod: warning in matrix(rnorm(q * nsim), nc = nsim): partial
  argument match of 'nc' to 'ncol'
simulate.merMod: warning in matrix(rnorm(n * nsim), nc = nsim): partial
  argument match of 'nc' to 'ncol'
splom.thpr : dp: warning in panel.axis(side = side, at = at, labels =
  format(at, trim = TRUE), tick = TRUE, check.overlap = TRUE, half =
  side == "top" && j > 1, tck = 1, rot = 0, text.col = axis.text.col,
  text.alpha = axis.text.alpha, text.cex = axis.text.cex, text.font =
  axis.text.font, text.fontfamily = axis.text.fontfamily, text.fontface
  = axis.text.fontface, line.col = axis.line.col, line.alpha =
  axis.line.alpha, line.lty = axis.line.lty, line.lwd = axis.line.lwd):
  partial argument match of 'tick' to 'ticks'
splom.thpr : dp: warning in panel.axis(side = side, at = at, labels =
  format(at, trim = TRUE), tick = TRUE, half = TRUE, which.half =
  which.half, tck = 1, rot = 0, text.col = axis.text.col, text.alpha =
  axis.text.alpha, text.cex = axis.text.cex, text.font =
  axis.text.font, text.fontfamily = axis.text.fontfamily, text.fontface
  = axis.text.fontface, line.col = axis.line.col, line.alpha =
  axis.line.alpha, line.lty = axis.line.lty, line.lwd = axis.line.lwd):
  partial argument match of 'tick' to 'ticks'
updateMod: warning in determinant(fe@fac, log = TRUE): partial argument
  match of 'log' to 'logarithm'
getME: no visible binding for global variable ‘....’
getME: no visible binding for global variable ‘.....re’
getME: no visible binding for global variable ‘....re’
log.thpr: no visible binding for global variable ‘.par’
splom.thpr: no visible binding for global variable ‘.par’
varianceProf: no visible binding for global variable ‘.par’
varpr: no visible binding for global variable ‘.par’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘VarCorr’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... ERROR
Running examples in ‘lme4a-Ex.R’ failed
The error most likely occurred in:

> ### Name: Dyestuff
> ### Title: Yield of dyestuff by batch
> ### Aliases: Dyestuff Dyestuff2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## Don't show: 
>  # useful for the lme4-authors --- development, debugging, etc:
>  commandArgs()[-1]
[1] "--vanilla"
>  if(FALSE) ## R environment variables:
+  local({ ne <- names(e <- Sys.getenv())
+          list(R    = e[grep("^R", ne)],
+               "_R" = e[grep("^_R",ne)]) })
>  Sys.getenv("R_ENVIRON")
[1] ""
>  Sys.getenv("R_PROFILE")
[1] ""
>  cat("R_LIBS:\n"); (RL <- strsplit(Sys.getenv("R_LIBS"), ":")[[1]])
R_LIBS:
[1] "/tmp/RtmpkDfbiI/RLIBS_23bc40e52b33"
>  nRL <- normalizePath(RL)
>  cat("and extra .libPaths():\n")
and extra .libPaths():
>  .libPaths()[is.na(match(.libPaths(), nRL))]
[1] "/srv/R/R-patched/build.13-02-14/library"
> 
>  sessionInfo()
R version 2.15.2 Patched (2013-02-13 r61942)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lme4a_0.9996875-1  MatrixModels_0.3-1 minqa_1.2.1        Rcpp_0.10.2       
[5] Matrix_1.0-11      lattice_0.20-13   

loaded via a namespace (and not attached):
[1] codetools_0.2-8 grid_2.15.2     nlme_3.1-108    splines_2.15.2 
>  pkgI <- function(pkgname) {
+    pd <- packageDescription(pkgname)
+    cat(sprintf("%s -- built: %s\n%*s -- dir  : %s\n",
+                pkgname, pd$Built, nchar(pkgname), "",
+                dirname(dirname(attr(pd, "file")))))
+  }
>  pkgI("Matrix")
Matrix -- built: R 2.15.2; x86_64-unknown-linux-gnu; 2013-02-08 19:15:07 UTC; unix
       -- dir  : /home/rforge/lib/R/2.15/Matrix
>  pkgI("Rcpp")
Rcpp -- built: R 2.15.2; x86_64-unknown-linux-gnu; 2013-02-07 15:15:59 UTC; unix
     -- dir  : /home/rforge/lib/R/2.15/Rcpp
>  pkgI("minqa")
minqa -- built: R 2.15.2; x86_64-unknown-linux-gnu; 2013-02-15 08:36:54 UTC; unix
      -- dir  : /home/rforge/lib/R/2.15/minqa
>  pkgI("MatrixModels")
MatrixModels -- built: R 2.15.2; ; 2013-02-15 08:18:53 UTC; unix
             -- dir  : /home/rforge/lib/R/2.15/MatrixModels
>  pkgI("lme4a")
lme4a -- built: R 2.15.2; x86_64-unknown-linux-gnu; 2013-02-15 12:39:39 UTC; unix
      -- dir  : /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4a.Rcheck/lme4a
> ## End Don't show
> str(Dyestuff)
'data.frame':	30 obs. of  2 variables:
 $ Batch: Factor w/ 6 levels "A","B","C","D",..: 1 1 1 1 1 2 2 2 2 2 ...
 $ Yield: num  1545 1440 1440 1520 1580 ...
> dotplot(reorder(Batch, Yield) ~ Yield, Dyestuff,
+         ylab = "Batch", jitter.y = TRUE, aspect = 0.3,
+         type = c("p", "a"))
> dotplot(reorder(Batch, Yield) ~ Yield, Dyestuff2,
+         ylab = "Batch", jitter.y = TRUE, aspect = 0.3,
+         type = c("p", "a"))
> (fm1 <- lmer(Yield ~ 1|Batch, Dyestuff))
Error: is.numeric(u <- attr(fval, "u")) is not TRUE
Execution halted
Run time: 623.31 seconds.