• using R version 2.11.1 Patched (2010-07-29 r52657)
• using session charset: ISO8859-1
• checking for file 'phyclust/DESCRIPTION' ... OK
• this is package 'phyclust' version '0.1-8'
• checking package name space information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking whether package 'phyclust' 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 package can be unloaded cleanly ... OK
• checking whether the name space can be loaded with stated dependencies ... OK
• checking whether the name space 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
  chkdim.Add.fun: no visible binding for global variable 'RRstar'
  get.deriBigMatB.fun: no visible binding for global variable 'k'
  get.fullBB.fun: no visible binding for global variable 'medBB.cs'
  get.fullBB.fun: no visible binding for global variable 'subPI.cs'
  get.matD.matEI.fun: no visible binding for global variable 'y'
  get.matD.matEI.fun: no visible binding for global variable 'mu'
  get.matD.matEI.fun: no visible binding for global variable 'a'
  get.matD.matEI.fun: no visible binding for global variable 'xRD.post'
  get.matD.matEI.fun: no visible binding for global variable 'x.post'
  get.matD.matEI.fun: no visible binding for global variable 'xRD'
  get.matD.matEI.fun: no visible binding for global variable 'x'
  get.matD.matEI.fun: no visible binding for global variable 'post'
  get.matD.matEI.fun: no visible binding for global variable 'v'
  get.matD.matEI.fun: no visible binding for global variable 'nreps'
  get.matD.matEI.fun: no visible binding for global variable 'CC'
  get.matD.matEI.fun: no visible binding for global variable 'subPI'
  get.matD.matEI.fun: no visible binding for global variable 'BB'
  get.matD.matEI.fun: no visible binding for global variable 'p.cscn.FD'
  get.matD.matEI.fun: no visible binding for global variable 'x.adj'
  get.medBB.skip.fun: no visible binding for global variable 'subPI.cn'
  get.medBB.skip.fun: no visible binding for global variable 'preBB.cn'
  get.medBB.skip.fun: no visible binding for global variable 'indexBB.cn'
  get.preBB.skip.fun: no visible binding for global variable 'subPI.cs'
  getBigMatB.fun: no visible binding for global variable 'BB.cs'
  getBigMatB.fun: no visible binding for global variable 'subPI.cs'
  getI13.fun: no visible binding for global variable 'y'
  getPIstar.fun: no visible binding for global variable 'BB.cs'
  getPIstar.fun: no visible binding for global variable 'subPI.cs'
  getcut.fun: no visible binding for global variable 'nhap'
  haplo.score.RD.unphased.fun: no visible binding for global variable
  'Y.vec'
  haplo.score.RD.unphased.fun: no visible binding for global variable
  'Geno'
  haplo.score.RD.unphased.fun: no visible global function definition for
  'haplo.em'
  haplo.score.RD.unphased.fun: no visible global function definition for
  'haplo.em.control'
  haplo.score.RD.unphased.fun: no visible binding for global variable
  'nhap'
  haplo.score.RD.unphased.fun: no visible binding for global variable
  'digit'
  haplo.score.RD.unphased.fun: no visible global function definition for
  'Ginv'
• 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 data for non-ASCII characters ... 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 ... OK
• checking examples ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking PDF version of manual ... OK