* using log directory 'd:/Rcompile/CRANpkg/local/2.13/qtlbim.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'qtlbim/DESCRIPTION' ... OK
* this is package 'qtlbim' version '1.9.4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'qtlbim' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 'd:/RCompile/CRANpkg/local/2.13/qtlbim/man/diag.Rd':
  '[base]{boxplot}'

Missing link(s) in documentation object 'd:/RCompile/CRANpkg/local/2.13/qtlbim/man/loci.Rd':
  '[graphics]{jitter}' '[base]{plot}'

Missing link(s) in documentation object 'd:/RCompile/CRANpkg/local/2.13/qtlbim/man/plot.Rd':
  '[base]{plot}'

Missing link(s) in documentation object 'd:/RCompile/CRANpkg/local/2.13/qtlbim/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 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                  old_size new_size compress
  Bnapus.RData        18Kb     12Kb    bzip2
  fisch.RData         14Kb      9Kb    bzip2
  qbExample.RData    262Kb    180Kb       xz
  qbHyper.RData      543Kb    350Kb       xz
  qbSimEpi.RData      94Kb     63Kb       xz
  qbSimMain.RData     79Kb     54Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'FIG-QBCODA.pdf' from 294Kb to 65Kb
     compacted 'FIG-QBEPI.pdf' from 195Kb to 23Kb
     compacted 'FIG-QBLOCI34.pdf' from 234Kb to 25Kb
     compacted 'FIG-Scantwo-HyperData.pdf' from 395Kb to 48Kb
     compacted 'mult.pdf' from 520Kb to 111Kb
     compacted 'multmerge.pdf' from 268Kb to 69Kb
     compacted 'prototype.qtl.hyper.slides.pdf' from 429Kb to 145Kb
     compacted 'qtlbim.pdf' from 2356Kb to 606Kb
     compacted 'slide2LOD-1.pdf' from 151Kb to 20Kb
  consider running tools::compactPDF() on these files
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... OK
* checking re-building of vignettes ... OK
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
  'd:/Rcompile/CRANpkg/local/2.13/qtlbim.Rcheck/00check.log'
for details