• using R Under development (unstable) (2012-08-11 r60235)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘NestedCohort/DESCRIPTION’ ... OK
• this is package ‘NestedCohort’ version ‘1.1-2’
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... NOTE
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
  CRAN requires a NAMESPACE file for all submissions.
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking whether package ‘NestedCohort’ 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 ... NOTE
  Found the following CITATION file(s) in a non-standard place:
  CITATION
  Most likely ‘inst/CITATION’ should be used instead.
• 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 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
  nested.coxph: no visible binding for global variable ‘p.i.h.a.t.’
  nested.km: no visible binding for global variable ‘p.i.h.a.t.’
  nested.stdsurv: no visible binding for global variable ‘p.i.h.a.t.’
• 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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... NOTE
  The following files look like leftovers/mistakes:
  ‘NestedCohort.bbl’
  Please remove them from your package.
  The following files should probably not be installed:
  ‘S.sty’
  The following directories should probably not be installed:
  ‘auto’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [2s/2s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [2s/2s] OK
• checking re-building of vignette PDFs ... NOTE
  Error in re-building vignettes:
  ...
  "legend.pos" is not a graphical parameter
  Warning in box(...) : "legend.text" is not a graphical parameter
  Warning in box(...) : "legend.pos" is not a graphical parameter
  Warning in title(...) : "legend.text" is not a graphical parameter
  Warning in title(...) : "legend.pos" is not a graphical parameter
  Warning in coxph(as.formula(coxformula), weights = 1/p.i.h.a.t., method = "breslow", :
  The robust option is depricated
  Warning in coxph(as.formula(coxformula), weights = 1/p.i.h.a.t., method = "breslow", :
  The robust option is depricated
  Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
  Running 'texi2dvi' on 'NestedCohort.tex' failed.
  LaTeX errors:
  ! LaTeX Error: File `psfig.sty' not found.
  
  Type X to quit or <RETURN> to proceed,
  or enter new name. (Default extension: sty)
  
  ! Emergency stop.
  <read *>
  
  l.11 \newcommand
  {\bex}{\begin{Example}}^^M
  ! ==> Fatal error occurred, no output PDF file produced!
  Calls: buildVignettes -> texi2pdf -> texi2dvi
  Execution halted
  
• checking PDF version of manual ... OK
  NOTE: There were 5 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/NestedCohort.Rcheck/00check.log’
  for details.