• using R version 2.15.0 Patched (2012-03-31 r58888)
• using platform: sparc-sun-solaris2.10 (32-bit)
• using session charset: UTF-8
• checking for file ‘SNPassoc/DESCRIPTION’ ... OK
• this is package ‘SNPassoc’ version ‘1.8-1’
• package encoding: latin1
• 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 .dll and .exe files ... OK
• checking whether package ‘SNPassoc’ can be installed ... OK
• checking installed package size ... OK
• 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 ... NOTE
  maxstat.matrix : pmax: warning in pmvnorm(lower, upper, mean, cor =
  sqrt(corr), ...): partial argument match of 'cor' to 'corr'
  plot.SNPinteraction: warning in axis(1, at = c(1:nrow(x.OK)), label =
  label.SNPs, las = 3, cex.axis = 0.7, col = "darkgreen"): partial
  argument match of 'label' to 'labels'
  plot.SNPinteraction: warning in axis(2, at = c(1:nrow(x.OK)), label =
  label.SNPs, las = 1, cex.axis = 0.7, col = "darkgreen"): partial
  argument match of 'label' to 'labels'
  plot.WGassociation: warning in axis(1, at = c(1:length(xx)), label =
  rep("", length(xx)), pos = 0): partial argument match of 'label' to
  'labels'
  plot.WGassociation: warning in axis(2, at = control.y, label =
  -control.y, pos = 1, xaxt = "n"): partial argument match of 'label'
  to 'labels'
  plotMissing: warning in axis(1, at = c(1:length(label.SNPs)), label =
  label.SNPs, las = 3, cex.axis = 0.7): partial argument match of
  'label' to 'labels'
  Found .Internal call in the following function:
  ‘scanWGassociation’
  with calls to .Internal functions
  ‘unlist’
  
  Packages should not call .Internal(): it is not part of the API, for
  use only by R itself and subject to change without notice.
• checking Rd files ... NOTE
  prepare_Rd: LD.Rd:69-71: Dropping empty section \examples
  prepare_Rd: plotWGassociation.Rd:64-66: Dropping empty section \examples
• 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 ... 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 compiled code ... OK
• checking examples ... ERROR
  Running examples in ‘SNPassoc-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: GenomicControl
  > ### Title: Population substructure
  > ### Aliases: GenomicControl
  > ### Keywords: utilities
  >
  > ### ** Examples
  >
  >
  > data(SNPs)
  > datSNP<-setupSNP(SNPs,6:40,sep="")
  > res<-scanWGassociation(casco,datSNP,model=c("do","re","log-add"))
  Be patient. The program is computing ...
  The program took 0.08 seconds
  >
  > # Genomic Control
  > resCorrected<-GenomicControl(res)
  
  lambda:
  dominant recessive log-additive
  NA NA 0.1219302
  > plot(resCorrected)
  Error in xy.coords(x, y, xlabel, ylabel, log) :
  'x' and 'y' lengths differ
  Calls: plot ... plot.WGassociation -> plot -> plot.default -> xy.coords
  Execution halted