• using R version 2.14.1 Patched (2012-02-07 r58290)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘qtl/DESCRIPTION’ ... OK
• this is package ‘qtl’ version ‘1.22-21’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package ‘qtl’ can be installed ... OK
• checking installed package size ... NOTE
  installed size is 6.2Mb
  sub-directories of 1Mb or more:
  docs 3.4Mb
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... 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 whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... 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 ... OK
• checking Rd files ... OK
• 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 ... NOTE
  S3 methods shown with full name in documentation object 'plot.errorlod':
  ‘plot.errorlod’
  
  S3 methods shown with full name in documentation object 'plot.geno':
  ‘plot.geno’
  
  S3 methods shown with full name in documentation object 'plot.info':
  ‘plot.info’
  
  S3 methods shown with full name in documentation object 'plot.map':
  ‘plot.map’
  
  S3 methods shown with full name in documentation object 'plot.missing':
  ‘plot.missing’
  
  S3 methods shown with full name in documentation object 'plot.pheno':
  ‘plot.pheno’
  
  S3 methods shown with full name in documentation object 'plot.pxg':
  ‘plot.pxg’
  
  S3 methods shown with full name in documentation object 'plot.rf':
  ‘plot.rf’
  
  S3 methods shown with full name in documentation object 'summary.map':
  ‘summary.map’
  
  S3 methods shown with full name in documentation object 'summary.scantwo.old':
  ‘summary.scantwo.old’
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See the chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking examples ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ... OK
  Running ‘test_io.R’
  Comparing ‘test_io.Rout’ to ‘test_io.Rout.save’ ... OK
  Running ‘test_qtl.R’
  Running ‘testaugmentation.R’
• checking PDF version of manual ... OK