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lme4b log file (check_x86_64_linux)

Fri Feb 15 12:48:09 2013: Checking package lme4b (SVN revision 1040) ...
* using log directory ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4b.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 ‘lme4b/DESCRIPTION’ ... OK
* this is package ‘lme4b’ version ‘0.999375-60’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Douglas Bates ’
New submission
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘src’ contains:
  GLfamily.hpp lme4utils.hpp matrix.hpp merenv.hpp
These are unlikely file names for src files.
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking whether package ‘lme4b’ can be installed ... [17s/67s] WARNING
Found the following significant warnings:
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4b.Rcheck/00_pkg_src/lme4b/man/fixef.Rd: docType ‘genericFunction’ is unrecognized
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4b.Rcheck/00_pkg_src/lme4b/man/ranef.Rd: Multiple \docType sections are not supported
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4b.Rcheck/00_pkg_src/lme4b/man/ranef.Rd: docType ‘genericFunction’ is unrecognized
  Warning: value of 'strip.white' option should be lowercase
  Warning: S3 methods ‘plot.coef.mer’, ‘dotplot.coef.mer’, ‘plot.ranef.mer’, ‘qqmath.ranef.mer’, ‘dotplot.ranef.mer’ were declared in NAMESPACE but not found
See ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4b.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 ... OK
* 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 ... WARNING
Warning: declared S3 method ‘plot.coef.mer’ not found
Warning: declared S3 method ‘plot.ranef.mer’ not found
Warning: declared S3 method ‘dotplot.coef.mer’ not found
Warning: declared S3 method ‘dotplot.ranef.mer’ not found
Warning: declared S3 method ‘qqmath.ranef.mer’ not found
See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
anovaLmer: warning in pchisq(chisq, dfChisq, lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
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'
makeZt : mkBlist: warning in matrix(seq_len(nc * nl), nc = nl, byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
makeZt : : warning in matrix(seq_len(nb[i]), nc = nc[i],
  byrow = TRUE): partial argument match of 'nc' to 'ncol'
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'
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'
anova,lmer: warning in pchisq(chisq, dfChisq, lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
anova,lmerenv: warning in pchisq(chisq, dfChisq, lower = FALSE):
  partial argument match of 'lower' to 'lower.tail'
plot,lmList.confint-ANY: warning in gl(dd[3], dd[1] * dd[2], len = ll,
  lab = dn[[3]]): partial argument match of 'len' to 'length'
plot,lmList.confint-ANY: warning in gl(dd[3], dd[1] * dd[2], len = ll,
  lab = dn[[3]]): partial argument match of 'lab' to 'labels'
plot,lmList.confint-ANY: warning in gl(dd[2], dd[1], len = ll): partial
  argument match of 'len' to 'length'
.setPars: no visible binding for global variable ‘compDev’
.setPars: no visible binding for global variable ‘theta’
.setPars: no visible binding for '<<-' assignment to ‘theta’
.setPars: no visible binding for '<<-' assignment to ‘Lambda’
.setPars: no visible binding for global variable ‘Lambda’
.setPars: no visible binding for global variable ‘Lind’
.setPars: no visible binding for '<<-' assignment to ‘Ut’
.setPars: no visible binding for global variable ‘Zt’
.setPars: no visible binding for global variable ‘L’
.setPars: no visible binding for global variable ‘Ut’
.setPars: no visible binding for global variable ‘Utr’
.setPars: no visible binding for '<<-' assignment to ‘RZX’
.setPars: no visible binding for global variable ‘UtV’
.setPars: no visible binding for global variable ‘sparseX’
.setPars: no visible binding for '<<-' assignment to ‘RX’
.setPars: no visible binding for global variable ‘RX’
.setPars: no visible binding for global variable ‘VtV’
.setPars: no visible binding for global variable ‘RZX’
.setPars: no visible binding for global variable ‘Vtr’
.setPars: no visible binding for '<<-' assignment to ‘u’
.setPars: no visible binding for global variable ‘u’
.setPars: no visible binding for '<<-' assignment to ‘mu’
.setPars: no visible binding for global variable ‘mu’
.setPars: no visible binding for global variable ‘X’
.setPars: no visible binding for '<<-' assignment to ‘pwrss’
.setPars: no visible binding for global variable ‘y’
.setPars: no visible binding for '<<-' assignment to ‘ldL2’
.setPars: no visible binding for global variable ‘ldL2’
.setPars: no visible binding for global variable ‘REML’
.setPars: no visible binding for '<<-' assignment to ‘ldRX2’
.setPars: no visible binding for global variable ‘ldRX2’
.setPars: no visible binding for global variable ‘nmp’
.setPars: no visible binding for global variable ‘pwrss’
anovaLmer: no visible binding for global variable
  ‘mer_update_projection’
glmer1: no visible global function definition for ‘model.Matrix’
glmer1 : gP: no visible binding for global variable ‘theta’
glmer1 : gB: no visible binding for global variable ‘lower’
lmer1: no visible global function definition for ‘model.Matrix’
lmer1 : gP: no visible binding for global variable ‘theta’
lmer1 : gB: no visible binding for global variable ‘lower’
lmer1 : gB: no visible binding for global variable ‘theta’
log.thpr: no visible binding for global variable ‘.par’
nlmer1: no visible global function definition for ‘model.Matrix’
nlmer1: no visible global function definition for ‘getBounds’
nlmer1: no visible global function definition for ‘getPars’
nlmer1: no visible global function definition for ‘setPars’
splom.thpr: no visible binding for global variable ‘.par’
varpr: no visible binding for global variable ‘.par’
anova,lmer: no visible binding for global variable
  ‘mer_update_projection’
anova,lmerenv: no visible binding for global variable
  ‘mer_update_projection’
* checking Rd files ... WARNING
prepare_Rd: fixef.Rd: docType ‘genericFunction’ is unrecognized
prepare_Rd: ranef.Rd: Multiple \docType sections are not supported
prepare_Rd: ranef.Rd: docType ‘genericFunction’ is unrecognized
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4b.Rcheck/00_pkg_src/lme4b/man/lmer.Rd’:
  ‘mer-class’

Missing link(s) in documentation object ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/lme4b.Rcheck/00_pkg_src/lme4b/man/ranef.Rd’:
  ‘mer-class’

See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.

* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘glmer’ ‘lmer’ ‘mer’
Undocumented S4 methods:
  generic 'VarCorr' and siglist 'mer'
  generic 'anova' and siglist 'lmer'
  generic 'coef' and siglist 'mer'
  generic 'coerce' and siglist 'lmerenv,lmer'
  generic 'deviance' and siglist 'lmer'
  generic 'deviance' and siglist 'mer'
  generic 'formula' and siglist 'mer'
  generic 'logLik' and siglist 'lmer'
  generic 'logLik' and siglist 'mer'
  generic 'model.frame' and siglist 'mer'
  generic 'model.matrix' and siglist 'mer'
  generic 'optimize' and siglist 'merenv'
  generic 'print' and siglist 'mer'
  generic 'profile' and siglist 'lmer'
  generic 'profile' and siglist 'lmerenv'
  generic 'show' and siglist 'mer'
  generic 'sigma' and siglist 'mer'
  generic 'summary' and siglist 'mer'
  generic 'terms' and siglist 'mer'
  generic 'update' and siglist 'mer'
  generic 'vcov' and siglist 'mer'
All user-level objects in a package (including S4 classes and methods)
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 ‘lme4b-Ex.R’ failed
The error most likely occurred in:

> ### Name: Dyestuff
> ### Title: Yield of dyestuff by batch
> ### Aliases: Dyestuff Dyestuff2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 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 <- lmer1(Yield ~ 1|Batch, Dyestuff))
Error in lmer1(Yield ~ 1 | Batch, Dyestuff) : 
  could not find function "model.Matrix"
Execution halted
Run time: 484.34 seconds.