• using R Under development (unstable) (2012-02-07 r58290)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘lme4/DESCRIPTION’ ... OK
• this is package ‘lme4’ version ‘0.999375-42’
• 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 whether package ‘lme4’ can be installed ... [15s/22s] OK
• 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 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 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
  nlmer : <anonymous>: warning in assign(nm, env = env, mf[[nm]]):
  partial argument match of 'env' to 'envir'
  nlmer : <anonymous>: warning in assign(nm, env = env,
  rep(start$fixef[[nm]], length.out = n)): partial argument match of
  'env' to 'envir'
  printMer: warning in abbreviate(rn, minlen = 11): partial argument
  match of 'minlen' to 'minlength'
  printMer: 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'
  printMer: warning in abbreviate(rn, minlen = 6): partial argument match
  of 'minlen' to 'minlength'
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• 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 ... [18s/25s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [88s/120s] OK
  Running ‘Gamma.R’ [8s/11s]
  Running ‘drop.R’
  Running ‘extras.R’
  Running ‘lmer-1.R’ [9s/12s]
  Comparing ‘lmer-1.Rout’ to ‘lmer-1.Rout.save’ ... OK
  Running ‘lmer-conv.R’
  Running ‘lmer.R’
  Running ‘nlmer-conv.R’ [24s/32s]
  Running ‘nlmer.R’ [24s/33s]
  Comparing ‘nlmer.Rout’ to ‘nlmer.Rout.save’ ...6d5
  < > ## TODO: nicer version of this is in system.file("test-tools.R", package = "Matrix")
  Running ‘simulate.R’
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [11s/15s] OK
• checking re-building of vignette PDFs ... [16s/30s] OK
• checking PDF version of manual ... OK
  NOTE: There was 1 note.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/lme4.Rcheck/00check.log’
  for details.