* using log directory 'd:/Rcompile/CRANpkg/local/2.15/scaRabee.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'scaRabee/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scaRabee' version '1.1-2'
* 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 whether package 'scaRabee' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
File 'scaRabee/R/zzz.R':
  .onLoad calls:
    require(lattice)
    require(grid)
    require(deSolve)
    require(neldermead)
    require(utils)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

fitmle: warning in fminsearch(fun = obj.fun, x = x0, options =
  options): partial argument match of 'x' to 'x0'
scarabee.read.data: no visible binding for global variable 'TRT'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'bound.parameters.tex', 'compute.secondary.tex',
  'convert.infusion.tex', 'create.intervals.tex', 'dde.model.tex',
  'dde.utils.tex', 'estimation.plot.tex', 'examples.data.tex',
  'explicit.model.tex', 'finalize.grid.report.tex',
  'finalize.report.tex', 'fitmle.cov.tex', 'fitmle.tex',
  'get.cov.matrix.tex', 'get.events.tex', 'get.layout.tex',
  'get.param.data.tex', 'get.parms.data.tex', 'get.secondary.tex',
  'initialize.report.tex', 'ode.model.tex', 'ode.utils.tex',
  'order.param.list.tex', 'order.parms.list.tex', 'pder.tex',
  'problem.eval.tex', 'residual.report.tex', 'scaRabee-package.tex',
  'scarabee.analysis.tex', 'scarabee.check.model.tex',
  'scarabee.check.reserved.tex', 'scarabee.clean.tex',
  'scarabee.directory.tex', 'scarabee.gridsearch.tex',
  'scarabee.new.tex', 'scarabee.read.data.tex',
  'scarabee.read.model.tex', 'scarabee.read.parms.tex',
  'simulation.plot.tex', 'simulation.report.tex', 'weighting.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... OK
* checking re-building of vignette PDFs ... OK
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/scaRabee.Rcheck/00check.log'
for details.