* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘haplotypes’ ... ** 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 finding level-2 HTML links ... done 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)