• using R version 2.15.0 (2012-03-30)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘ape/DESCRIPTION’ ... OK
• this is package ‘ape’ version ‘3.0-3’
• 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 whether package ‘ape’ 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 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
  .getRHOetINT : INT: no visible binding for global variable ‘Tmax’
  CADM.post: no visible binding for global variable ‘p’
  as.igraph.phylo: no visible global function definition for
  ‘graph.edgelist’
  as.network.phylo: no visible global function definition for ‘network’
  as.network.phylo: no visible global function definition for
  ‘network.vertex.names<-’
  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 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 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) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [24s/24s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [1s/1s] OK
• checking re-building of vignette PDFs ... [2s/3s] OK
• checking PDF version of manual ... OK
  NOTE: There was 1 note.
  See
  ‘/home/hornik/tmp/R.check/r-release/Work/PKGS/ape.Rcheck/00check.log’
  for details.