* using log directory 'd:/Rcompile/CRANpkg/local/2.12/ape.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'ape/DESCRIPTION' ... OK
* this is package 'ape' version '2.8'
* 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 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 ... NOTE
'library' or 'require' call not declared from: vegan
* 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) and $(LAPACK_LIBS) ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking PDF version of manual ... OK