• 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.