• using R Under development (unstable) (2012-02-06 r58287)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘msm/DESCRIPTION’ ... OK
• this is package ‘msm’ version ‘1.1’
• 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 whether package ‘msm’ 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
  dpexp: warning in pexp(dt, rate[-length(rate)], log = TRUE, lower.tail
  = FALSE): partial argument match of 'log' to 'log.p'
• 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 'plot.prevalence.msm':
  ‘plot.prevalence.msm’
  
  S3 methods shown with full name in documentation object 'plot.survfit.msm':
  ‘plot.survfit.msm’
  
  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 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 compilation flags in Makevars ... 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 installed files from ‘inst/doc’ ... OK
• checking examples ... [10s/10s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [257s/258s] OK
  Running ‘analyticp.R’ [1s/1s]
  Running ‘boot.R’ [0s/0s]
  Running ‘deriv-debug.R’ [0s/0s]
  Running ‘deriv-test.R’ [0s/0s]
  Running ‘deriv.R’ [2s/2s]
  Running ‘errors.R’ [16s/16s]
  Running ‘fev.R’ [3s/3s]
  Running ‘herrors.R’ [1s/1s]
  Running ‘hsim.R’ [1s/1s]
  Running ‘local.R’ [0s/0s]
  Running ‘misc.R’ [6s/6s]
  Running ‘miscnew.R’ [1s/1s]
  Running ‘pci.R’ [188s/189s]
  Running ‘pearson.R’ [18s/18s]
  Running ‘sim.R’ [0s/0s]
  Running ‘simple.R’ [19s/19s]
  Running ‘utils.R’ [0s/1s]
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/msm.Rcheck/00check.log’
  for details.