* using log directory 'd:/Rcompile/CRANpkg/local/2.15/NestedCohort.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'NestedCohort' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 for left-overs from vignette generation ... WARNING
  file 'inst/doc/Rplots.ps', 'inst/doc/Rplots.pdf' will not be installed: please remove it
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 ... NOTE
Error in re-building vignettes:
  ...
  "legend.text" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "legend.pos" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "legend.text" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "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
Warning: running command '"d:\compiler\texmf\miktex\bin\texi2dvi.exe" --quiet --pdf "NestedCohort.tex"  -I "d:/RCompile/recent/R-2.15.0/share/texmf/tex/latex" -I "d:/RCompile/recent/R-2.15.0/share/texmf/bibtex/bst"' had status 1
Error: 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)

Execution halted

* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/NestedCohort.Rcheck/00check.log'
for details.