• using R version 2.13.0 Under development (unstable) (2011-03-11 r54733)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• 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 for executable files ... OK
• checking whether package 'qtlbim' can be installed ... OK
• checking installed package size ... NOTE
  installed size is 7.6Mb
  sub-directories of 1Mb or more:
  doc 5.1Mb
• 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
• 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 name space can be loaded with stated dependencies ... OK
  ** checking whether the name space can be unloaded cleanly ... OK
• loading checks for arch 'ppc'
  ** 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
• loading checks for arch 'x86_64'
  ** 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 '/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.13/qtlbim.Rcheck/00_pkg_src/qtlbim/man/diag.Rd':
  '[base]{boxplot}'
  
  Missing link(s) in documentation object '/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.13/qtlbim.Rcheck/00_pkg_src/qtlbim/man/loci.Rd':
  '[graphics]{jitter}' '[base]{plot}'
  
  Missing link(s) in documentation object '/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.13/qtlbim.Rcheck/00_pkg_src/qtlbim/man/plot.Rd':
  '[base]{plot}'
  
  Missing link(s) in documentation object '/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.13/qtlbim.Rcheck/00_pkg_src/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 ... OK
• 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 24Kb
  compacted 'FIG-QBLOCI34.pdf' from 234Kb to 26Kb
  compacted 'FIG-Scantwo-HyperData.pdf' from 395Kb to 48Kb
  compacted 'mult.pdf' from 520Kb to 112Kb
  compacted 'multmerge.pdf' from 268Kb to 70Kb
  compacted 'prototype.qtl.hyper.slides.pdf' from 429Kb to 268Kb
  compacted 'qtlbim.pdf' from 2356Kb to 644Kb
  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 'ppc' ... OK
  ** running examples for arch 'x86_64' ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning, see
  '/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.13/qtlbim.Rcheck/00check.log'
  for details
• elapsed time (check, wall clock): 5:45