• using R Under development (unstable) (2012-08-14 r60253)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘Mangrove/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘Mangrove’ version ‘1.1’
• 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 for hidden files and directories ... 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 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 loading without being on the library search path ... 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 ... 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 ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘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
  NOTE: There was 1 note.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/Mangrove.Rcheck/00check.log’
  for details.