• using R Under development (unstable) (2012-02-27 r58511)
• using platform: x86_64-pc-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'LIM/DESCRIPTION' ... OK
• this is package 'LIM' version '1.4.2'
• 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 'LIM' 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 ... OK
• 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 ... NOTE
  S3 methods shown with full name in documentation object 'Ldei':
  'Ldei.lim' 'Ldei.limfile' 'Ldei.character' 'Ldei.double'
  
  S3 methods shown with full name in documentation object 'Linp':
  'Linp.lim' 'Linp.limfile' 'Linp.character' 'Linp.double'
  
  S3 methods shown with full name in documentation object 'Lsei':
  'Lsei.double' 'Lsei.lim' 'Lsei.limfile' 'Lsei.character'
  
  S3 methods shown with full name in documentation object 'Setup':
  'Setup.limfile' 'Setup.character' 'Setup.liminput'
  
  S3 methods shown with full name in documentation object 'Plotranges':
  'Plotranges.double' 'Plotranges.lim'
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See the chapter 'Writing R documentation files' in the 'Writing R
  Extensions' manual.
• 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' ... NOTE
  'qpdf' made some significant size reductions:
  compacted 'FigReaction.pdf' from 527Kb to 103Kb
  compacted 'Figblending.pdf' from 256Kb to 56Kb
  compacted 'LIM.pdf' from 1075Kb to 376Kb
  compacted 'LIMecoli.pdf' from 1133Kb to 329Kb
  consider running tools::compactPDF() on these files
• checking installed files from 'inst/doc' ... NOTE
  The following files are already in R: 'jss.bst', 'jss.cls'
  Please remove them from your package.
• checking examples ...
  ** running examples for arch 'i386' ... WARNING
  Found the following significant warnings:
  
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Deprecated functions may be defunct as soon as of the next release of
  R.
  See ?Deprecated.
  ** running examples for arch 'x64' ... WARNING
  Found the following significant warnings:
  
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Deprecated functions may be defunct as soon as of the next release of
  R.
  See ?Deprecated.
• 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
  WARNING: There were 2 warnings.
  NOTE: There were 3 notes.
  See
  'd:/Rcompile/CRANpkg/local/2.15/LIM.Rcheck/00check.log'
  for details.