* using log directory 'd:/Rcompile/CRANpkg/local/2.7/qtl.Rcheck' * using R version 2.7.2 (2008-08-25) * using session charset: ISO8859-1 * checking for file 'qtl/DESCRIPTION' ... OK * this is package 'qtl' version '1.09-43' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'qtl' can be installed ... OK * 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 ... OK * checking Rd files ... 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.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.missing': plot.missing 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 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 compilation flags in Makevars ... OK * checking for portable use of $BLAS_LIBS ... OK * creating qtl-Ex.R ... OK * checking examples ... OK * checking tests ... OK * creating qtl-manual.tex ... OK * checking qtl-manual.tex using pdflatex ... OK