• using R Under development (unstable) (2012-08-11 r60235)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• 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 for executable files ... OK
• checking for hidden files and directories ... 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 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 loading without being on the library search path ... 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 ... [19s/20s] OK
• checking PDF version of manual ... OK
  NOTE: There was 1 note.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/MADAM.Rcheck/00check.log’
  for details.