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robustDist log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2013-07-18-00-09/RF_PKG_CHECK/PKGS/robustDist.Rcheck'
* using R version 3.0.1 Patched (2013-07-15 r63328)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'robustDist/DESCRIPTION' ... OK
* this is package 'robustDist' version '1.0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Vladimir N. Minin '
New submission
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'robustDist' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
as.eigen:
  function(x, ...)
as.eigen.default:
  function(x)

as.eigen:
  function(x, ...)
as.eigen.revmc:
  function(x)

See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
codonHKY.model: no visible global function definition for
  'convert10to4'
fit.hky: no visible global function definition for 'as.eigen.hky'
fit.hky: no visible binding for global variable 'aux.sum2'
fit.hky: no visible binding for global variable 'aux.sum3'
fit.hky: no visible binding for global variable 'aux.sum4'
fit.poisson: no visible global function definition for 'two.state.mc'
pair.likelihood.hky: no visible global function definition for
  'hky.model'
robust.codon.dist: no visible global function definition for
  'ind.codon.mc'
robust.f84: no visible binding for global variable 'mc.size'
robust.jc: possible error in fit.jc(mc.stat, pair.seq): unused argument
  (pair.seq)
robust.jc: no visible binding for global variable 'mc.stat'
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'TTV' 'as.eigen' 'as.eigen.default' 'as.eigen.revmc' 'as.revmc'
  'codon.to.amino' 'codon.to.dna' 'codon.to.dna.align' 'codonHKY.model'
  'codonTest' 'conv.dist' 'conv.f84' 'conv.jc' 'count.pair.patterns'
  'count.pair.patterns.old' 'count.unique.sites' 'dna.to.codon'
  'dna.to.codon.align' 'emp.freq' 'extended.count.pair.patterns'
  'f84.mc' 'fit.f84' 'fit.hky' 'fit.jc' 'fit.mc' 'fit.poisson'
  'get.f84.rates' 'gtr.mc' 'hky.mc' 'increment' 'ind.codon.eigen'
  'is.nonsyn.mutation' 'is.single.mutation' 'is.syn.mutation' 'jc.mc'
  'joint.mean.markov.jumps' 'kronecker.sum' 'matexp' 'pair.conv.dist'
  'pair.likelihood.hky' 'pair.log.like' 'pair.log.like.old'
  'pair.robust.dist' 'pair.robust.dist.old' 'read.phylip'
  'regist.nonsynonym' 'regist.nonsynonym.ts' 'regist.nonsynonym.tv'
  'regist.synonym' 'regist.synonym.ts' 'regist.synonym.tv'
  'resample.codon' 'rescale.mc' 'robust.codon.dist'
  'robust.codon.dist.f84' 'robust.codon.dist.f84.pos.1.2.3'
  'robust.codon.dist.f84.pos.12.3' 'robust.codon.dist.f84.pos.123'
  'robust.codon.dist.new' 'robust.codon.dist.onef84' 'robust.dN.dS'
  'robust.dist' 'robust.f84' 'robust.jc' 'sim.pair.align'
  'site.pair.counts' 'site.pair.likelihood'
  'stat.marg.mean.markov.jumps'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
  'R:/run/building/build_2013-07-18-00-09/RF_PKG_CHECK/PKGS/robustDist.Rcheck/00check.log'
for details.

Run time: 36.46 seconds.