• using R version 2.10.0 Patched (2009-11-05 r50317)
• 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: ./man/Bnapus.Rd:35: unknown macro '\item'
  Warning: ./man/Bnapus.Rd:36: unknown macro '\item'
  Warning: ./man/Bnapus.Rd:37: unknown macro '\item'
  Warning: ./man/Bnapus.Rd:38: unknown macro '\item'
  Warning: ./man/Bnapus.Rd:43: unknown macro '\item'
  Warning: ./man/Bnapus.Rd:47: unknown macro '\item'
  Warning: ./man/Bnapus.Rd:48: unknown macro '\item'
  Warning: ./man/Bnapus.Rd:52: unknown macro '\item'
  Warning: ./man/Bnapus.Rd:58: unknown macro '\item'
  Warning: bad markup (extra space?) at bim.qtl.Rd:38:13
  Warning: ./man/read.bim.Rd:41: unexpected '}'
  Warning: ./man/run.bmapqtl.Rd:52: unknown macro '\item'
  Warning: ./man/run.bmapqtl.Rd:53: unknown macro '\item'
  Warning: ./man/run.bmapqtl.Rd:59: unknown macro '\item'
  Warning: ./man/run.bmapqtl.Rd:68: unknown macro '\item'
  Warning: ./man/vern.Rd:28: unknown macro '\item'
  Warning: ./man/vern.Rd:29: unknown macro '\item'
  Warning: ./man/vern.Rd:33: unknown macro '\item'
  Warning: ./man/vern.Rd:38: unknown macro '\item'
  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 ... WARNING
  prepare_Rd: Bnapus.Rd:35: unknown macro '\item'
  prepare_Rd: Bnapus.Rd:36: unknown macro '\item'
  prepare_Rd: Bnapus.Rd:37: unknown macro '\item'
  prepare_Rd: Bnapus.Rd:38: unknown macro '\item'
  prepare_Rd: Bnapus.Rd:43: unknown macro '\item'
  prepare_Rd: Bnapus.Rd:47: unknown macro '\item'
  prepare_Rd: Bnapus.Rd:48: unknown macro '\item'
  prepare_Rd: Bnapus.Rd:52: unknown macro '\item'
  prepare_Rd: Bnapus.Rd:58: unknown macro '\item'
  prepare_Rd: bad markup (extra space?) at bim.qtl.Rd:38:13
  checkRd: (5) bmapqtl.options.Rd:53: Tag \eqn is invalid in a \code block
  prepare_Rd: read.bim.Rd:41: unexpected '}'
  prepare_Rd: run.bmapqtl.Rd:52: unknown macro '\item'
  prepare_Rd: run.bmapqtl.Rd:53: unknown macro '\item'
  prepare_Rd: run.bmapqtl.Rd:59: unknown macro '\item'
  prepare_Rd: run.bmapqtl.Rd:68: unknown macro '\item'
  prepare_Rd: vern.Rd:28: unknown macro '\item'
  prepare_Rd: vern.Rd:29: unknown macro '\item'
  prepare_Rd: vern.Rd:33: unknown macro '\item'
  prepare_Rd: vern.Rd:38: unknown macro '\item'
• checking Rd metadata ... OK
• checking Rd cross-references ... WARNING
  Obsolete package(s) ‘modreg’ in Rd xrefs
  Missing link(s) in documentation object './man/bim.effects.Rd':
  ‘[base]{plot}’
  
  Missing link(s) in documentation object './man/bim.fdr.Rd':
  ‘[base]{plot}’
  
  Missing link(s) in documentation object './man/bim.qtl.Rd':
  ‘[base]{plot}’
  
  Missing link(s) in documentation object './man/plot.bim.Rd':
  ‘[base]{plot}’
  
  Missing link(s) in documentation object './man/plot.bim.diag.Rd':
  ‘[base]{plot}’ ‘[base]{boxplot}’
  
  Missing link(s) in documentation object './man/plot.bim.loci.Rd':
  ‘[base]{plot}’
  
  Missing link(s) in documentation object './man/plot.bim.mcmc.Rd':
  ‘[base]{plot}’
  
  Missing link(s) in documentation object './man/plot.bim.model.Rd':
  ‘[base]{plot}’
  
  See the information in section 'Cross-references' of the 'Writing R
  Extensions' manual.
  
• 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