* using log directory 'd:/Rcompile/CRANpkg/local/2.10/ComPairWise.Rcheck'
* using R version 2.10.0 RC (2009-10-20 r50178)
* using session charset: ISO8859-1
* checking for file 'ComPairWise/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ComPairWise' version '1.01'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ComPairWise' can be installed ... WARNING
Found the following significant warnings:
  Warning: ./man/ComPairWise-package.Rd:21: unknown macro '\item'
  Warning: ./man/ComPairWise-package.Rd:23: unknown macro '\item'
  Warning: ./man/ComPairWise-package.Rd:25: unknown macro '\item'
  Warning: ./man/ComPairWise-package.Rd:27: unknown macro '\item'
  Warning: ./man/cpw.Rd:37: unknown macro '\item'
  Warning: ./man/cpw.Rd:41: unknown macro '\item'
  Warning: ./man/cpw.Rd:43: unknown macro '\item'
  Warning: ./man/cpw.Rd:45: unknown macro '\item'
  Warning: ./man/cpw.Rd:47: unknown macro '\item'
  Warning: ./man/cpw.Rd:49: unknown macro '\item'
  Warning: ./man/cpw.Rd:51: unknown macro '\item'
  Warning: ./man/cpw.Rd:53: unknown macro '\item'
  Warning: ./man/cpw.Rd:55: unknown macro '\item'
  Warning: ./man/cpw.Rd:57: unknown macro '\item'
  Warning: ./man/cpw.Rd:59: unknown macro '\item'
  Warning: ./man/cpw.Rd:61: unknown macro '\item'
  Warning: ./man/cpw.Rd:63: unknown macro '\item'
  Warning: ./man/cpw.Rd:65: unknown macro '\item'
  Warning: ./man/cpw.Rd:76: unknown macro '\item'
  Warning: ./man/cpw.Rd:77: unknown macro '\item'
  Warning: ./man/cpw.Rd:78: unknown macro '\item'
  Warning: ./man/cpw.Rd:79: unknown macro '\item'
  Warning: ./man/cpw.Rd:80: unknown macro '\item'
  Warning: ./man/endpoints.Rd:18: unexpected '}'
See 'd:/Rcompile/CRANpkg/local/2.10/ComPairWise.Rcheck/00install.out' for details.
* 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
* 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
cpw: no visible binding for '<<-' assignment to 'filenames'
Found possibly global 'T' or 'F' in the following functions:
  check.format cpw dots.to.bases read.nexus read.phylip
* checking Rd files ... WARNING
prepare_Rd: ComPairWise-package.Rd:21: unknown macro '\item'
prepare_Rd: ComPairWise-package.Rd:23: unknown macro '\item'
prepare_Rd: ComPairWise-package.Rd:25: unknown macro '\item'
prepare_Rd: ComPairWise-package.Rd:27: unknown macro '\item'
prepare_Rd: cpw.Rd:37: unknown macro '\item'
prepare_Rd: cpw.Rd:41: unknown macro '\item'
prepare_Rd: cpw.Rd:43: unknown macro '\item'
prepare_Rd: cpw.Rd:45: unknown macro '\item'
prepare_Rd: cpw.Rd:47: unknown macro '\item'
prepare_Rd: cpw.Rd:49: unknown macro '\item'
prepare_Rd: cpw.Rd:51: unknown macro '\item'
prepare_Rd: cpw.Rd:53: unknown macro '\item'
prepare_Rd: cpw.Rd:55: unknown macro '\item'
prepare_Rd: cpw.Rd:57: unknown macro '\item'
prepare_Rd: cpw.Rd:59: unknown macro '\item'
prepare_Rd: cpw.Rd:61: unknown macro '\item'
prepare_Rd: cpw.Rd:63: unknown macro '\item'
prepare_Rd: cpw.Rd:65: unknown macro '\item'
prepare_Rd: cpw.Rd:76: unknown macro '\item'
prepare_Rd: cpw.Rd:77: unknown macro '\item'
prepare_Rd: cpw.Rd:78: unknown macro '\item'
prepare_Rd: cpw.Rd:79: unknown macro '\item'
prepare_Rd: cpw.Rd:80: unknown macro '\item'
prepare_Rd: endpoints.Rd:18: unexpected '}'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking PDF version of manual ... OK