• using R version 2.9.1 Patched (2009-07-02 r48890)
• using session charset: UTF-8
• 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: unmatched right brace in file 'read.bim.Rd' on line 41
  See http://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/bim-00install.html for details.
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... NOTE
  Non-standard license specification:
  GPL version 2 or newer
  Standardizable: TRUE
  Standardized license specification:
  GPL (>= 2)
• 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