• using R Under development (unstable) (2012-02-27 r58511)
• using platform: x86_64-pc-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'Mangrove/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'Mangrove' version '1.0'
• 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 'Mangrove' 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
• 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
  .addNode: no visible binding for global variable 'private'
  .addNode: no visible binding for '<<-' assignment to 'private'
  .addPed: no visible binding for '<<-' assignment to 'private'
  .addPed: no visible binding for global variable 'private'
  .addPed: no visible binding for global variable 'public'
  .addPed : <anonymous>: no visible binding for global variable 'public'
  .addRoot: no visible binding for global variable 'private'
  .addRoot: no visible binding for '<<-' assignment to 'private'
  .calcAlpha: no visible binding for global variable 'private'
  .calcAlpha: no visible binding for '<<-' assignment to 'private'
  .calcAlpha: no visible binding for global variable 'public'
  .calcAlpha : <anonymous>: no visible binding for global variable
  'private'
  .calcBeta: no visible binding for global variable 'private'
  .calcBeta: no visible binding for '<<-' assignment to 'private'
  .calcBeta : <anonymous>: no visible binding for global variable
  'private'
  .calcBeta: no visible binding for global variable 'public'
  .calcLikelihoods: no visible binding for '<<-' assignment to 'private'
  .calcLikelihoods: no visible binding for global variable 'private'
  .calcParams: no visible binding for global variable 'tree'
  .calcPost: no visible binding for global variable 'private'
  .calcPost: no visible binding for '<<-' assignment to 'private'
  .calcPost: no visible binding for global variable 'public'
  .getData: no visible binding for global variable 'private'
  .getMaxDepth: no visible binding for global variable 'public'
  .getNNodes: no visible binding for global variable 'private'
  .getNinds: no visible binding for global variable 'private'
  .getOffspring: no visible binding for global variable 'private'
  .getPrevs: no visible binding for global variable 'public'
  .getPrevs: no visible binding for '<<-' assignment to 'private'
  .getPrevs: no visible binding for global variable 'private'
  .getRoot: no visible binding for global variable 'private'
  .getTrans: no visible binding for global variable 'mendT'
  .printSummary: no visible binding for global variable 'public'
  .printSummary: no visible binding for global variable 'private'
  .printTree: no visible binding for global variable 'public'
  .sampleCases: no visible binding for global variable 'private'
  .sampleCases: no visible binding for '<<-' assignment to 'private'
  .sampleVariant: no visible binding for global variable 'private'
  .sampleVariant: no visible binding for '<<-' assignment to 'private'
  .sampleVariant: no visible binding for global variable 'public'
  .sampleVariants: no visible binding for '<<-' assignment to 'private'
  .sampleVariants: no visible binding for global variable 'private'
  .sampleVariants: no visible binding for global variable 'public'
  initialiseTree: no visible binding for global variable 'mendT'
• 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 'MangroveORs':
  'print.MangroveORs' 'summary.MangroveORs' 'plot.MangroveORs'
  
  S3 methods shown with full name in documentation object 'MangrovePed':
  'summary.MangrovePed' 'print.MangrovePed' 'plot.MangrovePed'
  
  S3 methods shown with full name in documentation object 'MangroveRiskPreds':
  'print.MangroveRiskPreds' 'summary.MangroveRiskPreds'
  'plot.MangroveRiskPreds'
  
  S3 methods shown with full name in documentation object 'MangroveSample':
  'print.MangroveSample' 'summary.MangroveSample' 'plot.MangroveSample'
  
  S3 methods shown with full name in documentation object 'MangroveTree':
  'print.MangroveTree' 'summary.MangroveTree' 'plot.MangroveTree'
  
  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
  ccped.rda 198Kb 58Kb xz
• checking sizes of PDF files under 'inst/doc' ... OK
• checking installed files from 'inst/doc' ... OK
• checking examples ...
  ** running examples for arch 'i386' ... OK
  ** running examples for arch 'x64' ... 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
  WARNING: There was 1 warning.
  NOTE: There were 2 notes.
  See
  'd:/Rcompile/CRANpkg/local/2.15/Mangrove.Rcheck/00check.log'
  for details.