* using log directory 'd:/Rcompile/CRANpkg/local/2.9/bim.Rcheck'
* using R version 2.9.2 Patched (2009-09-02 r49531)
* using session charset: ISO8859-1
* checking for file 'bim/DESCRIPTION' ... OK
* this is package 'bim' version '1.01-5'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'bim' can be installed ... WARNING
Found the following significant warnings:
  Warning: invalid whitespace before brace in file 'bim.qtl.Rd' at ' \item{hpd} {density critical values for high probability density (HPD) region}'
  Warning: invalid whitespace before brace in file 'bim.qtl.Rd' at ' \item{hpd} {density critical values for high probability density (HPD) region}'
  Warning: unmatched right brace in file 'read.bim.Rd' on line 41
  Warning: unmatched right brace in file 'read.bim.Rd' on line 41
See 'd:/Rcompile/CRANpkg/local/2.9/bim.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
bmapqtl.options: no visible binding for global variable
  '.bmapqtl.options'
bmapqtl.options: no visible binding for '<<-' assignment to
  '.bmapqtl.options'
bmapqtl.options.init: no visible binding for '<<-' assignment to
  '.bmapqtl.options'
bmapqtl.options.init: no visible binding for global variable
  '.bmapqtl.options'
read.bim: ... may be used in an incorrect context: read.table(bimfile,
  header = TRUE, na.strings = na.strings, skip = skip, fill = TRUE,
  nrows = nrows, ...)
read.bmapqtl: no visible binding for '<<-' assignment to
  '.bmapqtl.options'
read.bmapqtl: no visible binding for global variable '.bmapqtl.options'
run.bmapqtl: no visible binding for global variable '.bmapqtl.options'
write.bmapqtl: no visible binding for global variable
  '.bmapqtl.options'
Warning: <anonymous>: ... may be used in an incorrect context: 
     read.table(bimfile, header = TRUE, na.strings = na.strings, skip = skip, 
         fill = TRUE, nrows = nrows, ...)

Found possibly global 'T' or 'F' in the following function:
  run.bmapqtl
* checking Rd files ... OK
* checking Rd files against version 2 parser ... WARNING
*** error on file ./man/Bnapus.Rd
Error : ./man/Bnapus.Rd:35: Unrecognized macro \item

Warning in parse_Rd("./man/bim.qtl.Rd", encoding = "unknown") :
  bad markup (extra space?) at bim.qtl.Rd:38:13
Warning: ./man/bim.qtl.Rd:38: Unnecessary braces at '{density critical values for high probability density (HPD) region}'
*** error on file ./man/read.bim.Rd
Error in parse_Rd("./man/read.bim.Rd", encoding = "unknown") : 
  ./man/read.bim.Rd:41:1: unexpected '}'
40: }
41: }
    ^

*** error on file ./man/run.bmapqtl.Rd
Error : ./man/run.bmapqtl.Rd:52: Unrecognized macro \item

*** error on file ./man/vern.Rd
Error : ./man/vern.Rd:28: Unrecognized macro \item

problems found in 'Bnapus.Rd', 'read.bim.Rd', 'run.bmapqtl.Rd', 'vern.Rd'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'bim-internal':
  plot.bim.pattern

S3 methods shown with full name in documentation object 'bim.effects':
  plot.bim.effects

S3 methods shown with full name in documentation object 'bim.fdr':
  plot.bim.fdr

S3 methods shown with full name in documentation object 'bim.':
  plot.bim.qtl

S3 methods shown with full name in documentation object 'plot.bim':
  plot.bim

S3 methods shown with full name in documentation object 'plot.bim.diag':
  plot.bim.diag

S3 methods shown with full name in documentation object 'plot.bim.loci':
  plot.bim.loci

S3 methods shown with full name in documentation object 'plot.bim.mcmc':
  plot.bim.mcmc

S3 methods shown with full name in documentation object 'plot.bim.model':
  plot.bim.model

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking PDF version of manual ... OK