• 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 ‘polySegratioMM/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘polySegratioMM’ version ‘0.6-1’
• 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 ‘polySegratioMM’ can be installed ... 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
  plotFitted: warning in plotTheoretical(ploidy =
  model$E.segRatio$ploidy.level, n.comp = model$n.components,
  n.individuals = seg.ratios$n.individuals, proportions = eta, xaxis =
  pl.type): partial argument match of 'ploidy' to 'ploidy.level'
  plotFitted: warning in plotTheoretical(ploidy =
  model$E.segRatio$ploidy.level, n.comp = model$n.components,
  n.individuals = seg.ratios$n.individuals, proportions = eta, xaxis =
  pl.type): partial argument match of 'n.comp' to 'n.components'
  plotTheoretical: warning in expected.segRatio(ploidy.level, type =
  type): partial argument match of 'type' to 'type.parents'
  runSegratioMM: warning in diagnosticsJagsMix(read.jags, diagnostics =
  print.diagnostics, plot = plot.diagnostics, return.results = TRUE):
  partial argument match of 'plot' to 'plots'
  setModel: warning in expected.segRatio(ploidy.level, type = type):
  partial argument match of 'type' to 'type.parents'
• checking Rd files ... NOTE
  prepare_Rd: hexmarkers.overdisp.Rd:15: Dropping empty section \source
  prepare_Rd: mcmcHexRun.Rd:18: Dropping empty section \source
• 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 'plot.segratioMCMC':
  ‘plot.segratioMCMC’
  
  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 ... WARNING
  
  Note: significantly better compression could be obtained
  by using R CMD build --resave-data
  old_size new_size compress
  hexmarkers.RData 33Kb 18Kb bzip2
  hexmarkers.overdisp.RData 34Kb 19Kb bzip2
  mcmcHexRun.RData 284Kb 188Kb xz
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... NOTE
  The following directories should probably not be installed:
  ‘auto’, ‘tmp’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [1s/1s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [2s/2s] OK
• checking re-building of vignette PDFs ... [3s/3s] OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 4 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/polySegratioMM.Rcheck/00check.log’
  for details.