• using R version 2.14.2 (2012-02-29)
• using platform: i386-pc-mingw32 (32-bit)
• using session charset: ISO8859-1
• checking for file 'MeDiChI/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'MeDiChI' version '0.4.0'
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Packages suggested but not available for checking:
  'multicore' 'doMC'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking whether package 'MeDiChI' 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
• 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
  File 'MeDiChI/R/chip.deconv.pkg.R':
  .onLoad calls:
  cat("Loading MeDiChI, version ", VERSION, " (", DATE, ")\n", sep = "")
  
  Package startup functions should use 'packageStartupMessage' to
  generate messages.
  See section 'Good practice' in ?.onAttach.
  
  deconv.entire.genome : apply.func: no visible global function
  definition for '%dopar%'
  deconv.entire.genome : apply.func: no visible global function
  definition for 'foreach'
  deconv.entire.genome : apply.func: no visible binding for global
  variable 'l'
  deconv.entire.genome : <anonymous>: no visible binding for global
  variable 'ind'
  fit.peak.profile: no visible binding for global variable 'mclapply'
  generate.binding.profile : apply.func: no visible global function
  definition for '%dopar%'
  generate.binding.profile : apply.func: no visible global function
  definition for 'foreach'
  generate.binding.profile : apply.func: no visible binding for global
  variable 'l'
• 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 'chip.deconv':
  'plot.chip.deconv' 'print.chip.deconv' 'coef.chip.deconv'
  
  S3 methods shown with full name in documentation object 'deconv.entire.genome':
  'print.chip.deconv.entire.genome' 'plot.chip.deconv.entire.genome'
  'coef.chip.deconv.entire.genome'
  
  S3 methods shown with full name in documentation object 'fit.peak.profile':
  'plot.fit.peak.profile'
  
  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 ... NOTE
  
  Note: significantly better compression could be obtained
  by using R CMD build --resave-data
  old_size new_size compress
  halo.hires.rda 1.1Mb 593Kb xz
  halo.lowres.rda 356Kb 300Kb xz
  yeast.gcn4.rda 1.1Mb 698Kb xz
• checking sizes of PDF files under 'inst/doc' ... OK
• checking examples ... OK
• 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