• using R version 2.14.1 Patched (2012-02-04 r58267)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘depmixS4/DESCRIPTION’ ... OK
• this is package ‘depmixS4’ version ‘1.1-0’
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: ‘Rdonlp2’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package ‘depmixS4’ 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 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
  em.depmix: warning in matrix(runif(nr * ns, min = 1e-04, max = 0.9999),
  nr = nr, nc = ns): partial argument match of 'nr' to 'nrow'
  em.depmix: warning in matrix(runif(nr * ns, min = 1e-04, max = 0.9999),
  nr = nr, nc = ns): partial argument match of 'nc' to 'ncol'
  em.mix: warning in matrix(runif(nr * ns, min = 1e-04, max = 0.9999), nr
  = nr, nc = ns): partial argument match of 'nr' to 'nrow'
  em.mix: warning in matrix(runif(nr * ns, min = 1e-04, max = 0.9999), nr
  = nr, nc = ns): partial argument match of 'nc' to 'ncol'
  fb: warning in matrix(res$alpha, nc = ns, byrow = TRUE): partial
  argument match of 'nc' to 'ncol'
  fb: warning in matrix(res$beta, nc = ns, byrow = TRUE): partial
  argument match of 'nc' to 'ncol'
  makePriorModel: warning in transInit(~1, data = data.frame(rep(1,
  ncases)), nst = nstates, family = multinomial(link = "identity"),
  pstart = values): partial argument match of 'nst' to 'nstates'
  makePriorModel: warning in transInit(formula, data = data, nst =
  nstates, family = multinomial(), pstart = values): partial argument
  match of 'nst' to 'nstates'
• 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 line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking examples ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ... OK
  Running ‘test1speed.R’
  Comparing ‘test1speed.Rout’ to ‘test1speed.Rout.save’ ...8d7
  < Rsolnp (version 1.11) initialized.
  Running ‘test2getsetpars.R’
  Comparing ‘test2getsetpars.Rout’ to ‘test2getsetpars.Rout.save’ ...8d7
  < Rsolnp (version 1.11) initialized.
  Running ‘test3responses.R’
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... OK
• checking re-building of vignette PDFs ... OK
• checking PDF version of manual ... OK