* using log directory 'd:/Rcompile/CRANpkg/local/2.9/PhySim.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* checking for file 'PhySim/DESCRIPTION' ... OK
* this is package 'PhySim' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'PhySim' can be installed ... WARNING
Found the following significant warnings:
  Warning: unmatched right brace in file 'branchingPhySim.times.Rd' on line 10
  Warning: unmatched right brace in file 'branchingPhySim.times.Rd' on line 10
  Warning: unmatched right brace in file 'dropPhySim.tip.Rd' on line 10
  Warning: unmatched right brace in file 'dropPhySim.tip.Rd' on line 10
  Warning: unmatched right brace in file 'writePhySim.tree.Rd' on line 51
  Warning: unmatched right brace in file 'writePhySim.tree.Rd' on line 51
See 'd:/Rcompile/CRANpkg/local/2.9/PhySim.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... WARNING
Found the following file(s) with non-portable file names:
  functions details.txt
These are not fully portable file names
See section 'Package structure' in manual 'Writing R Extensions'.
* 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 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
dropPhySim.tip: no visible global function definition for 'write.tree'
dropPhySim.tip: no visible global function definition for 'clado.build'
dropPhySim.tip: no visible global function definition for 'tree.build'
readPhySim.tree: no visible global function definition for
  'clado.build'
* checking Rd files ... OK
* checking Rd files against version 2 parser ... WARNING
*** error on file ./man/branchingPhySim.times.Rd
Error in parse_Rd("./man/branchingPhySim.times.Rd", encoding = "unknown") : 
  ./man/branchingPhySim.times.Rd:10:1: unexpected '}'
9: \author{Emmanuel Paradis}
10: }
    ^

*** error on file ./man/dropPhySim.tip.Rd
Error in parse_Rd("./man/dropPhySim.tip.Rd", encoding = "unknown") : 
  ./man/dropPhySim.tip.Rd:10:1: unexpected '}'
9: \author{Emmanuel Paradis}
10: }
    ^

*** error on file ./man/writePhySim.tree.Rd
Error in parse_Rd("./man/writePhySim.tree.Rd", encoding = "unknown") : 
  ./man/writePhySim.tree.Rd:51:1: unexpected '}'
50: \seealso{\code{\link{readPhySim.tree}}, to read a phylogenetic tree from a file}
51: }
    ^

problems found in 'branchingPhySim.times.Rd', 'dropPhySim.tip.Rd', 'writePhySim.tree.Rd'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking examples ... OK
* checking PDF version of manual ... OK