• using R Under development (unstable) (2012-08-14 r60253)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘geiger/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘geiger’ version ‘1.3-1’
• 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 ‘geiger’ 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
  dtt.full: warning in sort(branching.times(td$phy), decr = TRUE):
  partial argument match of 'decr' to 'decreasing'
  fitContinuousModel: warning in optim(foo, p = start, lower = lower,
  upper = upper, method = "L"): partial argument match of 'p' to 'par'
  phy.anova: warning in sim.char(td$phy, as.matrix(s), nsim = nsim):
  partial argument match of 'nsim' to 'nsims'
  phy.manova: warning in sim.char(td$phy, s, nsim = nsim): partial
  argument match of 'nsim' to 'nsims'
• checking Rd files ... NOTE
  prepare_Rd: getAncStates.Rd:29: Dropping empty section \references
  prepare_Rd: medusa.Rd:60-62: Dropping empty section \seealso
  prepare_Rd: prune.extinct.taxa.Rd:21-22: Dropping empty section \details
  prepare_Rd: prune.extinct.taxa.Rd:26: Dropping empty section \references
  prepare_Rd: rate.estimate.Rd:36-37: Dropping empty section \details
  prepare_Rd: sim.char.Rd:35: Dropping empty section \references
  prepare_Rd: tip.disparity.Rd:16-17: Dropping empty section \details
• 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 ... [152s/153s] OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/geiger.Rcheck/00check.log’
  for details.