• using R version 3.0.1 Patched (2013-05-20 r62767)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘vegetarian/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘vegetarian’ version ‘1.2’
• 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 for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘vegetarian’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over 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
  H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
  M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
  Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
  bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of 'arg' to 'args'
  bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of 'arg' to
  'args'
  d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
  sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
  sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
  similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
  turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
• checking Rd files ... NOTE
  prepare_Rd: H.Rd:41-42: Dropping empty section \note
  prepare_Rd: M.homog.Rd:19-21: Dropping empty section \details
  prepare_Rd: M.homog.Rd:35-36: Dropping empty section \note
  prepare_Rd: Rel.homog.Rd:24-25: Dropping empty section \note
  prepare_Rd: bootstrap.Rd:34: Dropping empty section \note
  prepare_Rd: d.Rd:35-36: Dropping empty section \note
  prepare_Rd: normalize.rows.Rd:26-27: Dropping empty section \note
  prepare_Rd: p.q.sum.Rd:23-24: Dropping empty section \note
  prepare_Rd: p.q.sum.Rd:26: Dropping empty section \examples
  prepare_Rd: sim.groups.Rd:27-28: Dropping empty section \note
  prepare_Rd: sim.table.Rd:25-26: Dropping empty section \note
  prepare_Rd: similarity.Rd:25-26: Dropping empty section \note
  prepare_Rd: turnover.Rd:17-18: Dropping empty section \details
  prepare_Rd: turnover.Rd:29-30: Dropping empty section \note
• 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 ... [7s/7s] OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/home/hornik/tmp/R.check/r-patched-ng/Work/PKGS/vegetarian.Rcheck/00check.log’
  for details.