* using log directory 'd:/Rcompile/CRANpkg/local/2.8/Haplin.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'Haplin/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Haplin' version '3.0.1'
* package encoding: latin1
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Haplin' can be installed ... 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 ... OK
* 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 name space can be loaded with stated dependencies ... 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
f.jackknife.new: no visible global function definition for 'f.EM'
f.prep.data.new: possible error in f.sort.alleles.new(.mid, A =
  length(.alleles[[j]])): unused argument(s) (A =
  length(.alleles[[j]]))
f.prep.data.new: possible error in f.sort.alleles.new(.mid[i, ], A =
  length(.alleles[[j]])): unused argument(s) (A =
  length(.alleles[[j]]))
f.prep.data.new: no visible binding for global variable
  'f.sort.alleles'
f.prep.data.new : <anonymous>: no visible global function definition
  for 'f.sort.alleles'
f.prep.data.new: no visible global function definition for 'unpaste'
f.prep.data.new: multiple local function definitions for
  '.f.compute.pos' with different formal arguments
f.read.data: no visible global function definition for 'index.rowcol'
f.slide: no visible binding for global variable '.vcov.tot'
f.slide: no visible binding for global variable '.vcov.tot.just'
f.tri.glm: no visible binding for global variable '.cc'
haplin: no visible global function definition for 'f.sum.and.expand'
haplin: no visible binding for global variable '.prelim.haplotype.freq'
haplin: no visible binding for global variable '.haplotypes'
haplin: no visible binding for global variable '.temp'
haplin: no visible binding for global variable '.temp.0'
pedToHaplin: no visible binding for global variable 'mapfile'
pedToHaplin: no visible binding for global variable '.nfams'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating Haplin-Ex.R ... OK
* checking examples ... OK
* creating Haplin-manual.tex ... OK
* checking Haplin-manual.tex using pdflatex ... OK