• using R version 2.11.1 Patched (2010-07-29 r52657)
• using session charset: ISO8859-1
• checking for file 'DOSim/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'DOSim' version '2.0'
• checking package name space information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking whether package 'DOSim' can be installed ... 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
• 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 name space can be loaded with stated dependencies ... OK
• checking whether the name space 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
  DOEnrichment: no visible binding for global variable 'DOSimEnv'
  calcTermSim: no visible binding for global variable 'DOSimEnv'
  filterDO: no visible binding for global variable 'DOSimEnv'
  getAncestors: no visible binding for global variable 'DOSimEnv'
  getChildren: no visible binding for global variable 'DOSimEnv'
  getDOGraph: no visible binding for global variable 'DOSimEnv'
  getDefaultBackground: no visible binding for global variable 'DOSimEnv'
  getDisjCommAnc: no visible binding for global variable 'DOSimEnv'
  getDisjCommAncSim: no visible binding for global variable 'DOSimEnv'
  getDoAnno: no visible binding for global variable 'DOSimEnv'
  getDoTerm: no visible binding for global variable 'DOSimEnv'
  getGIC: no visible binding for global variable 'DOSimEnv'
  getMinimumSubsumer: no visible binding for global variable 'DOSimEnv'
  getOffsprings: no visible binding for global variable 'DOSimEnv'
  getParents: no visible binding for global variable 'DOSimEnv'
  getShortestPath: no visible binding for global variable 'DOSimEnv'
  getSimWang: no visible binding for global variable 'DOSimEnv'
  initialize: no visible binding for global variable 'DOSimEnv'
• 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 data for non-ASCII characters ... OK
• checking examples ... OK
• checking package vignettes in 'inst/doc' ... NOTE
  (Rterm.exe:2912): Pango-WARNING **: couldn't load font "Times New Not-Rotated 14", falling back to "Sans Not-Rotated 14", expect ugly output.
  checkVignettes(dir = 'd:/Rcompile/CRANpkg/local64/2.11/DOSim.Rcheck', workdir='src', tangle = FALSE, latex = TRUE)
• checking PDF version of manual ... OK