* using log directory 'd:/Rcompile/CRANpkg/local/2.11/qtlbim.Rcheck' * using R version 2.11.1 Patched (2010-07-29 r52657) * using session charset: ISO8859-1 * checking for file 'qtlbim/DESCRIPTION' ... OK * this is package 'qtlbim' version '1.9.4' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'qtlbim' 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 whether the package can be unloaded cleanly ... OK * checking whether the name space can be loaded with stated dependencies ... OK * checking whether the name space 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 ... NOTE qb.smoothsame: no visible binding for global variable 'smoothpair' qb.smoothtwo: multiple local function definitions for 'smoothpair' with different formal arguments * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Unknown package(s) 'code' in Rd xrefs Missing link(s) in documentation object './man/diag.Rd': '[base]{boxplot}' Missing link(s) in documentation object './man/loci.Rd': '[graphics]{jitter}' '[base]{plot}' Missing link(s) in documentation object './man/plot.Rd': '[base]{plot}' Missing link(s) in documentation object './man/qb-internal.Rd': '[base]{data}' 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 ... OK * checking Rd contents ... OK * 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