* using log directory 'd:/Rcompile/CRANpkg/local/2.15/rphast.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 'rphast/DESCRIPTION' ... OK
* this is package 'rphast' version '1.3'
* 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 whether package 'rphast' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       3.4Mb
    extdata   2.3Mb
    libs      1.9Mb
* 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 ... OK
* 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
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace 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 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 ... OK
* 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 'as.data.frame.feat':
  'as.data.frame.feat'

S3 methods shown with full name in documentation object 'as.list.tm':
  'as.list.tm'

S3 methods shown with full name in documentation object 'density.feat':
  'density.feat'

S3 methods shown with full name in documentation object 'dim.feat':
  'dim.feat'

S3 methods shown with full name in documentation object 'dim.msa':
  'dim.msa'

S3 methods shown with full name in documentation object 'hist.feat':
  'hist.feat'

S3 methods shown with full name in documentation object 'names.msa':
  'names.msa'

S3 methods shown with full name in documentation object 'plot.altmodel.tm':
  'plot.altmodel.tm'

S3 methods shown with full name in documentation object 'plot.feat':
  'plot.feat'

S3 methods shown with full name in documentation object 'plot.gene':
  'plot.gene'

S3 methods shown with full name in documentation object 'plot.msa':
  'plot.msa'

S3 methods shown with full name in documentation object 'plot.rate.matrix':
  'plot.rate.matrix'

S3 methods shown with full name in documentation object 'plot.tm':
  'plot.tm'

S3 methods shown with full name in documentation object 'plot.track':
  'plot.track'

S3 methods shown with full name in documentation object 'print.feat':
  'print.feat'

S3 methods shown with full name in documentation object 'print.msa':
  'print.msa'

S3 methods shown with full name in documentation object 'print.tm':
  'print.tm'

S3 methods shown with full name in documentation object 'range.feat':
  'range.feat'

S3 methods shown with full name in documentation object 'range.track':
  'range.track'

S3 methods shown with full name in documentation object 'simulate.msa':
  'simulate.msa'

S3 methods shown with full name in documentation object 'sort.feat':
  'sort.feat'

S3 methods shown with full name in documentation object 'split.by.feature.msa':
  'split.by.feature.msa'

S3 methods shown with full name in documentation object 'split.feat':
  'split.feat'

S3 methods shown with full name in documentation object 'summary.feat':
  'summary.feat'

S3 methods shown with full name in documentation object 'summary.msa':
  'summary.msa'

S3 methods shown with full name in documentation object 'summary.tm':
  'summary.tm'

S3 methods shown with full name in documentation object 'summary.tree':
  'summary.tree'

S3 methods shown with full name in documentation object 'unique.feat':
  'unique.feat'

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 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 ... NOTE
File 'd:/Rcompile/CRANpkg/lib/2.15/rphast/libs/i386/rphast.dll':
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'dgamma.o'
File 'd:/Rcompile/CRANpkg/lib/2.15/rphast/libs/x64/rphast.dll':
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'dgamma.o'

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'vignette1.pdf' from 308Kb to 163Kb
     compacted 'vignette3.pdf' from 2690Kb to 430Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... NOTE
The following files are already in R: 'Sweave.sty'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' OK
  Running 'feat.examples.R'
  Running 'hmm.examples.R'
  Running 'msa.examples.R'
  Running 'phastCons.examples.R'
  Running 'phyloFit.examples.R'
  Running 'phyloP.examples.R'
  Running 'plot.examples.R'
  Running 'treeModel.examples.R'
  Running 'trees.examples.R'
** running tests for arch 'x64' OK
  Running 'feat.examples.R'
  Running 'hmm.examples.R'
  Running 'msa.examples.R'
  Running 'phastCons.examples.R'
  Running 'phyloFit.examples.R'
  Running 'phyloP.examples.R'
  Running 'plot.examples.R'
  Running 'treeModel.examples.R'
  Running 'trees.examples.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
NOTE: There were 5 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/rphast.Rcheck/00check.log'
for details.