* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘ips’ ...
** this is package ‘ips’ version ‘0.0.12’
** package ‘ips’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘ips’
    finding HTML links ... done
    DNAbin2index                            html  
Rd warning: DNAbin2index.Rd:10: missing link ‘DNAbin’
    EmptyCells                              html  
Rd warning: EmptyCells.Rd:44: missing link ‘DNAbin’
Rd warning: EmptyCells.Rd:25: missing link ‘DNAbin’
Rd warning: EmptyCells.Rd:41: missing link ‘DNAbin’
    aliscore                                html  
    beastLog                                html  
    blastn                                  html  
    code.simple.gaps                        html  
Rd warning: code.simple.gaps.Rd:15: missing link ‘DNAbin’
Rd warning: code.simple.gaps.Rd:21: missing link ‘DNAbin’
    collapseUnsupportedEdges                html  
Rd warning: collapseUnsupportedEdges.Rd:10: missing link ‘phylo’
Rd warning: collapseUnsupportedEdges.Rd:19: missing link ‘phylo’
    combMyTree                              html  
Rd warning: combMyTree.Rd:10: missing link ‘phylo’
Rd warning: combMyTree.Rd:23: missing link ‘phylo’
    del.miss                                html  
Rd warning: del.miss.Rd:10: missing link ‘DNAbin’
    deleteGaps                              html  
Rd warning: deleteGaps.Rd:10: missing link ‘DNAbin’
Rd warning: deleteGaps.Rd:18: missing link ‘DNAbin’
    descendants                             html  
    fixNodes                                html  
Rd warning: fixNodes.Rd:9: missing link ‘phylo’
Rd warning: fixNodes.Rd:17: missing link ‘phylo’
Rd warning: fixNodes.Rd:27: missing link ‘phylo’
Rd warning: fixNodes.Rd:36: missing link ‘read.nexus’
    forceEqualTipHeights                    html  
Rd warning: forceEqualTipHeights.Rd:26: missing link ‘is.ultrametric’
Rd warning: forceEqualTipHeights.Rd:31: missing link ‘chronos’
    gblocks                                 html  
    index2DNAbin                            html  
Rd warning: index2DNAbin.Rd:10: missing link ‘DNAbin’
    ips-internal                            html  
    ips-package                             html  
Rd warning: ips-package.Rd:18: missing link ‘ladderize’
Rd warning: ips-package.Rd:18: missing link ‘rotate’
    ips.16S                                 html  
Rd warning: ips.16S.Rd:10: missing link ‘DNAbin’
    ips.28S                                 html  
Rd warning: ips.28S.Rd:12: missing link ‘DNAbin’
    ips.cox1                                html  
Rd warning: ips.cox1.Rd:12: missing link ‘DNAbin’
    ips.tree                                html  
    mafft                                   html  
Rd warning: mafft.Rd:53: missing link ‘phylo’
    mafft.merge                             html  
Rd warning: mafft.merge.Rd:10: missing link ‘DNAbin’
Rd warning: mafft.merge.Rd:11: missing link ‘AAbin’
Rd warning: mafft.merge.Rd:20: missing link ‘phylo’
Rd warning: mafft.merge.Rd:34: missing link ‘DNAbin’
Rd warning: mafft.merge.Rd:34: missing link ‘AAbin’
    mrbayes                                 html  
Rd warning: mrbayes.Rd:22: missing link ‘DNAbin’
    mrbayes.lset                            html  
    mrbayes.mcmc                            html  
    mrbayes.prset                           html  
    multistate                              html  
Rd warning: multistate.Rd:63: missing link ‘ace’
    neighboringPairs                        html  
Rd warning: neighboringPairs.Rd:10: missing link ‘mst’
    ntip                                    html  
Rd warning: ntip.Rd:10: missing link ‘phylo’
    oi                                      html  
    partitionfinder                         html  
    pathd8                                  html  
Rd warning: pathd8.Rd:10: missing link ‘phylo’
Rd warning: pathd8.Rd:22: missing link ‘phylo’
    phylo2mafft                             html  
Rd warning: phylo2mafft.Rd:10: missing link ‘phylo’
    phylo2mst                               html  
Rd warning: phylo2mst.Rd:10: missing link ‘phylo’
    pis                                     html  
Rd warning: pis.Rd:10: missing link ‘DNAbin’
    prank                                   html  
    raxml                                   html  
Rd warning: raxml.Rd:26: missing link ‘DNAbin’
Rd warning: raxml.Rd:57: missing link ‘phylo’
    raxml.partitions                        html  
Rd warning: raxml.partitions.Rd:11: missing link ‘DNAbin’
Rd warning: raxml.partitions.Rd:23: missing link ‘cbind.DNAbin’
    rbeauti                                 html  
Rd warning: rbeauti.Rd:22: missing link ‘DNAbin’
    rc                                      html  
    read                                    html  
Rd warning: read.Rd:56: missing link ‘cbind.DNAbin’
    read.beast                              html  
    read.beast.table                        html  
    sister                                  html  
Rd warning: sister.Rd:10: missing link ‘phylo’
    splitIntoClades                         html  
Rd warning: splitIntoClades.Rd:10: missing link ‘phylo’
    terminalSisters                         html  
Rd warning: terminalSisters.Rd:10: missing link ‘phylo’
    tipHeights                              html  
Rd warning: tipHeights.Rd:13: missing link ‘phylo’
Rd warning: tipHeights.Rd:23: missing link ‘branching.times’
    traitRate                               html  
Rd warning: traitRate.Rd:14: missing link ‘phylo’
Rd warning: traitRate.Rd:16: missing link ‘DNAbin’
Rd warning: traitRate.Rd:44: missing link ‘read.tree’
    trimEnds                                html  
    unlistFirstLevel                        html  
    write.fas                               html  
Rd warning: write.fas.Rd:26: missing link ‘DNAbin’
** 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 (ips)