• using R Under development (unstable) (2012-02-23 r58468)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• 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 for executable files ... OK
• checking whether package ‘CNVassoc’ can be installed ... OK
• checking installed package size ... NOTE
  installed size is 5.4Mb
  sub-directories of 1Mb or more:
  data 4.6Mb
• 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
  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’ ... OK
• 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 ... [14s/14s] 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 ... [1s/1s] WARNING
  Errors in running code in vignettes:
  when running code in ‘CNVassoc_vignette.Rnw’
  ...
  
  
  Loading required package: survival
  Loading required package: splines
  
  > library(xtable)
  
  When sourcing ‘CNVassoc_vignette.R’:
  Error: there is no package called ‘xtable’
  Execution halted
  
• checking re-building of vignette PDFs ... [62s/62s] OK
• checking PDF version of manual ... OK
  WARNING: There were 3 warnings.
  NOTE: There were 4 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/CNVassoc.Rcheck/00check.log’
  for details.