• using R Under development (unstable) (2012-02-24 r58481)
• using platform: x86_64-pc-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'CNVassoc/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'CNVassoc' version '1.0'
• package encoding: latin1
• 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 'CNVassoc' can be installed ... OK
• checking installed package size ... NOTE
  installed size is 5.1Mb
  sub-directories of 1Mb or more:
  data 3.7Mb
  doc 1.2Mb
• 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
  CNVtest: warning in pchisq(stat, df, lower = FALSE): partial argument
  match of 'lower' to 'lower.tail'
  anova.CNVassoc: warning in pchisq(abs(chi), abs(df), lower = FALSE):
  partial argument match of 'lower' to 'lower.tail'
• 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 ... WARNING
  
  Note: significantly better compression could be obtained
  by using R CMD build --resave-data
  old_size new_size compress
  NeveCalled.rda 1.0Mb 646Kb xz
  NeveData.rda 814Kb 472Kb xz
  NeveRegions.rda 14Kb 10Kb xz
  A112.RData 595Kb 423Kb xz
• checking for left-overs from vignette generation ... WARNING
  file 'inst/doc/Rplots.pdf' will not be installed: please remove it
• checking sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
  compacted 'CNVassoc_vignette.pdf' from 916Kb to 411Kb
  consider running tools::compactPDF() on these files
• checking installed files from 'inst/doc' ... NOTE
  The following files are already in R: 'Sweave.sty'
  Please remove them from your package.
  The following files look like leftovers/mistakes:
  'CNVassoc_vignette.bbl', 'CNVassoc_vignette.blg'
  Please remove them from your package.
  The following directories should probably not be installed:
  'figures'
  
  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 ... NOTE
  'library' or 'require' call not declared from: 'xtable'
• 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 5 notes.
  See
  'd:/Rcompile/CRANpkg/local/2.15/CNVassoc.Rcheck/00check.log'
  for details.