• using R version 2.9.1 Patched (2009-07-01 r48886)
• using session charset: UTF-8
• checking for file 'ape/DESCRIPTION' ... OK
• this is package 'ape' version '2.3-1'
• checking package name space information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking whether package 'ape' can be installed ... 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 name space can be loaded with stated dependencies ... 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
  CADM.post: no visible binding for global variable ‘p’
  birth.step: no visible global function definition for ‘loglik’
  death.step: no visible global function definition for ‘loglik’
  ht.move: no visible global function definition for ‘loglik’
  loglik.pop: no visible binding for global variable ‘b.lin’
  mcmc.popsize: no visible binding for '<<-' assignment to ‘loglik’
  mcmc.popsize: no visible global function definition for ‘loglik’
  plot.popsize: no visible binding for global variable ‘popsize’
  pos.move: no visible global function definition for ‘loglik’
• checking Rd files ... OK
• checking Rd files against version 2 parser ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking data for non-ASCII characters ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $BLAS_LIBS ... OK
• checking examples ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking PDF version of manual ... OK