• using R version 2.14.1 Patched (2012-02-05 r58287)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘titan/DESCRIPTION’ ... OK
• this is package ‘titan’ version ‘1.0-16’
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... NOTE
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
• checking for executable files ... OK
• checking whether package ‘titan’ 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 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
  titan : titan.widget : widget2: warning in matrix(FALSE, nr = ngene, nc
  = 2): partial argument match of 'nr' to 'nrow'
  titan : titan.widget : widget2: warning in matrix(FALSE, nr = ngene, nc
  = 2): partial argument match of 'nc' to 'ncol'
  titan : titan.widget : widget2: warning in matrix(FALSE, nr = ngene, nc
  = 1): partial argument match of 'nr' to 'nrow'
  titan : titan.widget : widget2: warning in matrix(FALSE, nr = ngene, nc
  = 1): partial argument match of 'nc' to 'ncol'
  titan : titan.input : data.levels : dummy: warning in matrix(nr = len,
  nc = nlevels): partial argument match of 'nr' to 'nrow'
  titan : titan.input : data.levels : dummy: warning in matrix(nr = len,
  nc = nlevels): partial argument match of 'nc' to 'ncol'
  titan : titan.input : data.levels: warning in matrix(nr =
  length(dat$x), nc = ncontr.rx): partial argument match of 'nr' to
  'nrow'
  titan : titan.input : data.levels: warning in matrix(nr =
  length(dat$x), nc = ncontr.rx): partial argument match of 'nc' to
  'ncol'
  titan : titan.create.formulae: warning in matrix(NA, nr =
  input$data$levels$ngene, nc = input$data$levels$ncontr.rx + 1):
  partial argument match of 'nr' to 'nrow'
  titan : titan.create.formulae: warning in matrix(NA, nr =
  input$data$levels$ngene, nc = input$data$levels$ncontr.rx + 1):
  partial argument match of 'nc' to 'ncol'
  titan : titan.interpolate: warning in matrix(NA, nr =
  length(gene.valid), nc = 1 + nrx1): partial argument match of 'nr' to
  'nrow'
  titan : titan.interpolate: warning in matrix(NA, nr =
  length(gene.valid), nc = 1 + nrx1): partial argument match of 'nc' to
  'ncol'
  titan : titan.interpolate: warning in matrix(NA, nr = ngene1, nc =
  nrx1): partial argument match of 'nr' to 'nrow'
  titan : titan.interpolate: warning in matrix(NA, nr = ngene1, nc =
  nrx1): partial argument match of 'nc' to 'ncol'
  titan : titan.interpolate: warning in matrix(NA, nr = ngene0, nc =
  nrx1): partial argument match of 'nr' to 'nrow'
  titan : titan.interpolate: warning in matrix(NA, nr = ngene0, nc =
  nrx1): partial argument match of 'nc' to 'ncol'
  titan : titan.interpolate: warning in matrix(colMeans(log10fold.g0), nr
  = ngene1, nc = nrx1, byrow = TRUE): partial argument match of 'nr' to
  'nrow'
  titan : titan.interpolate: warning in matrix(colMeans(log10fold.g0), nr
  = ngene1, nc = nrx1, byrow = TRUE): partial argument match of 'nc' to
  'ncol'
  titan : titan.bootstrap : boot.fun: warning in matrix(NA, nr = ngene0,
  nc = nrx1): partial argument match of 'nr' to 'nrow'
  titan : titan.bootstrap : boot.fun: warning in matrix(NA, nr = ngene0,
  nc = nrx1): partial argument match of 'nc' to 'ncol'
  titan : titan.bootstrap : boot.fun: warning in matrix(NA, nr = ngene1,
  nc = nrx1): partial argument match of 'nr' to 'nrow'
  titan : titan.bootstrap : boot.fun: warning in matrix(NA, nr = ngene1,
  nc = nrx1): partial argument match of 'nc' to 'ncol'
  titan : titan.bootstrap : boot.fun: warning in
  matrix(colMeans(theta.star.g0), nc = nrx1, nr = ngene1, byrow =
  TRUE): partial argument match of 'nr' to 'nrow'
  titan : titan.bootstrap : boot.fun: warning in
  matrix(colMeans(theta.star.g0), nc = nrx1, nr = ngene1, byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
  titan : titan.bootstrap.baselineonly : boot.fun: warning in matrix(NA,
  nr = (ngene1 - 1) * ngene1/2, nc = 1): partial argument match of 'nr'
  to 'nrow'
  titan : titan.bootstrap.baselineonly : boot.fun: warning in matrix(NA,
  nr = (ngene1 - 1) * ngene1/2, nc = 1): partial argument match of 'nc'
  to 'ncol'
  titan : print.titanboot: warning in matrix(NA, nr = len, nc = 7):
  partial argument match of 'nr' to 'nrow'
  titan : print.titanboot: warning in matrix(NA, nr = len, nc = 7):
  partial argument match of 'nc' to 'ncol'
• 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... OK
• checking PDF version of manual ... OK