• using R Under development (unstable) (2013-04-22 r62639)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘DOBAD/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘DOBAD’ version ‘1.0.1’
• 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 ... NOTE
  Found the following hidden files and directories:
  inst/doc/.Rhistory
  These were most likely included in error. See section ‘Package
  structure’ in the ‘Writing R Extensions’ manual.
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘DOBAD’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... NOTE
  File
  LICENSE
  is not mentioned in the DESCRIPTION file.
• 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
  CTMC.simulate: warning in matrix(0, nc = 2, nr = v.sz): partial
  argument match of 'nr' to 'nrow'
  CTMC.simulate: warning in matrix(0, nc = 2, nr = v.sz): partial
  argument match of 'nc' to 'ncol'
  CTMC.simulate: warning in matrix(0, nc = 2, nr = v.sz * 2): partial
  argument match of 'nr' to 'nrow'
  CTMC.simulate: warning in matrix(0, nc = 2, nr = v.sz * 2): partial
  argument match of 'nc' to 'ncol'
  addhold.joint.mean.one : secondDerivGen: warning in complex(real =
  myReal, im = myIm): partial argument match of 'im' to 'imaginary'
  bdARsimCondEnd: warning in apply(X = simCondArg, MARG = 1, FUN =
  function(SED) {: partial argument match of 'MARG' to 'MARGIN'
  bdARsimCondEnd: warning in bdARsimCondEnd.1(Naccepted = Naccepted,
  Ntotal = Ntotal, Nmax = Nmax, T = SED[3], a = SED[1], b = SED[2], L =
  L, m = m, nu = nu): partial argument match of 'MARG' to 'MARGIN'
  bdARsimCondEnd: warning in }): partial argument match of 'MARG' to
  'MARGIN'
  chooseSim.condBD.1.CTMC_PO_1: warning in apply(X = arg, MARG = 1, FUN =
  function(SED) {: partial argument match of 'MARG' to 'MARGIN'
  chooseSim.condBD.1.CTMC_PO_1: warning in chooseSim.condBD.1(T = SED[3],
  a = SED[1], b = SED[2], L = L, m = m, nu = nu, n.fft = n.fft,
  maxARsims = maxARsims): partial argument match of 'MARG' to 'MARGIN'
  chooseSim.condBD.1.CTMC_PO_1: warning in }): partial argument match of
  'MARG' to 'MARGIN'
  hold.joint.meanSq.one : secondDerivGen: warning in complex(re = myReal,
  im = myIm): partial argument match of 're' to 'real'
  hold.joint.meanSq.one : secondDerivGen: warning in complex(re = myReal,
  im = myIm): partial argument match of 'im' to 'imaginary'
  power.coef.many: warning in complex(real = 0, imag = 2 * pi): partial
  argument match of 'imag' to 'imaginary'
  power.coef.one: warning in complex(real = 0, imag = 2 * pi): partial
  argument match of 'imag' to 'imaginary'
  remhold.joint.mean.one : secondDerivGen: warning in complex(real =
  myReal, im = myIm): partial argument match of 'im' to 'imaginary'
  sim.condBD.main.CTMC_PO_1: warning in apply(X = simCondArg, MARG = 1,
  FUN = function(SED) {: partial argument match of 'MARG' to 'MARGIN'
  sim.condBD.main.CTMC_PO_1: warning in sim.condBD.1(T = SED[3], a =
  SED[1], b = SED[2], L = L, m = m, nu = nu, n.fft = n.fft): partial
  argument match of 'MARG' to 'MARGIN'
  sim.condBD.main.CTMC_PO_1: warning in }): partial argument match of
  'MARG' to 'MARGIN'
  sim.condBD.main.default: warning in apply(X = simCondArg, MARG = 1, FUN
  = function(SED) {: partial argument match of 'MARG' to 'MARGIN'
  sim.condBD.main.default: warning in sim.condBD.1(T = SED[3], a =
  SED[1], b = SED[2], L = L, m = m, nu = nu, n.fft = n.fft): partial
  argument match of 'MARG' to 'MARGIN'
  sim.condBD.main.default: warning in }): partial argument match of
  'MARG' to 'MARGIN'
  sim.condBD.main.list: warning in apply(X = simCondArg, MARG = 1, FUN =
  function(SED) {: partial argument match of 'MARG' to 'MARGIN'
  sim.condBD.main.list: warning in sim.condBD.1(T = SED[3], a = SED[1], b
  = SED[2], L = L, m = m, nu = nu, n.fft = n.fft): partial argument
  match of 'MARG' to 'MARGIN'
  sim.condBD.main.list: warning in }): partial argument match of 'MARG'
  to 'MARGIN'
• 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 ... NOTE
  S3 methods shown with full name in documentation object 'add.joint.mean.many':
  ‘all.cond.mean.PO’ ‘all.cond.mean2.PO’
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See the chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [186s/187s] OK
• checking re-building of vignette PDFs ... [199s/203s] OK
• checking PDF version of manual ... OK
  NOTE: There were 4 notes.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/DOBAD.Rcheck/00check.log’
  for details.