* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘haplotypes’ ...
** this is package ‘haplotypes’ version ‘1.1.3.2’
** package ‘haplotypes’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘haplotypes’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘haplotypes’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘haplotypes’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘haplotypes’
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘haplotypes’
Creating a generic function for ‘rownames<-’ from package ‘base’ in package ‘haplotypes’
in method for ‘as.dna’ with signature ‘"DNAbin"’: no definition for class “DNAbin”
in method for ‘as.dna’ with signature ‘"phyDat"’: no definition for class “phyDat”
Creating a generic function for ‘append’ from package ‘base’ in package ‘haplotypes’
in method for ‘pairnei’ with signature ‘"dist"’: no definition for class “dist”
in method for ‘pairPhiST’ with signature ‘"dist"’: no definition for class “dist”
in method for ‘haplotype’ with signature ‘"dist"’: no definition for class “dist”
Creating a new generic function for ‘grouping’ in package ‘haplotypes’
in method for ‘parsimnet’ with signature ‘"dist"’: no definition for class “dist”
** help
*** installing help indices
  converting help for package ‘haplotypes’
    finding HTML links ... done
    Dna-class                               html  
    Haplotype-class                         html  
    Parsimnet-class                         html  
    append-methods                          html  
    as.DNAbin-methods                       html  
    as.data.frame-methods                   html  
    as.dna-methods                          html  
    as.list-methods                         html  
    as.matrix-methods                       html  
    as.network-methods                      html  
    as.networx-methods                      html  
    as.numeric-methods                      html  
    as.phyDat-methods                       html  
    basecomp-methods                        html  
    boot.dna-methods                        html  
    distance-methods                        html  
    dna.obj                                 html  
    grouping-methods                        html  
    haplotype-methods                       html  
    haplotypes-internal                     html  
    haplotypes-package                      html  
    hapreord-methods                        html  
    homopoly-methods                        html  
    image-methods                           html  
    indelcoder-methods                      html  
    length-methods                          html  
    names-methods                           html  
    ncol-methods                            html  
    nrow-methods                            html  
    pairPhiST-methods                       html  
    pairnei-methods                         html  
    parsimnet-methods                       html  
    pielegend-methods                       html  
    pieplot-methods                         html  
    plot-methods                            html  
    polymorp-methods                        html  
    range-methods                           html  
    read.fas                                html  
    remove.gaps-methods                     html  
    rownames-methods                        html  
    show-methods                            html  
    subs-methods                            html  
    tolower-methods                         html  
    unique-methods                          html  
    z[-methods                              html  
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (haplotypes)