• using R Under development (unstable) (2012-02-27 r58511)
• using platform: x86_64-pc-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'MADAM/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'MADAM' version '1.1'
• 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 whether package 'MADAM' can be installed ... OK
• checking installed package size ... 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
• 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
  calculateRankProduct: warning in rank(RP.q, ties = "random"): partial
  argument match of 'ties' to 'ties.method'
  calculateRankSum: warning in rank(RS.q, ties = "random"): partial
  argument match of 'ties' to 'ties.method'
  doES: warning in rank(res$g2up$FDR, ties = "random"): partial argument
  match of 'ties' to 'ties.method'
  doES: warning in rank(res$g2down$FDR, ties = "random"): partial
  argument match of 'ties' to 'ties.method'
  doRhodesFDR: warning in rank(res$q.value, ties = "random"): partial
  argument match of 'ties' to 'ties.method'
  fisherMethod: warning in rank(res$q.value, ties = "random"): partial
  argument match of 'ties' to 'ties.method'
  plotFDR: warning in rank(order(x[, m]), ties = "random"): partial
  argument match of 'ties' to 'ties.method'
  plotFDR: warning in rank(data, ties = "first"): partial argument match
  of 'ties' to 'ties.method'
• checking Rd files ... OK
• 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 examples ...
  ** running examples for arch 'i386' ... OK
  ** running examples for arch 'x64' ... OK
• checking PDF version of manual ... OK
  NOTE: There was 1 note.
  See
  'd:/Rcompile/CRANpkg/local/2.15/MADAM.Rcheck/00check.log'
  for details.