Found the following significant warnings:
  Rd warning: DNAbin2index.Rd:10: missing link ‘DNAbin’
  Rd warning: EmptyCells.Rd:44: missing link ‘DNAbin’
  Rd warning: EmptyCells.Rd:25: missing link ‘DNAbin’
  Rd warning: EmptyCells.Rd:41: missing link ‘DNAbin’
  Rd warning: code.simple.gaps.Rd:15: missing link ‘DNAbin’
  Rd warning: code.simple.gaps.Rd:21: missing link ‘DNAbin’
  Rd warning: collapseUnsupportedEdges.Rd:10: missing link ‘phylo’
  Rd warning: collapseUnsupportedEdges.Rd:19: missing link ‘phylo’
  Rd warning: combMyTree.Rd:10: missing link ‘phylo’
  Rd warning: combMyTree.Rd:23: missing link ‘phylo’
  Rd warning: del.miss.Rd:10: missing link ‘DNAbin’
  Rd warning: deleteGaps.Rd:10: missing link ‘DNAbin’
  Rd warning: deleteGaps.Rd:18: missing link ‘DNAbin’
  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’
  Rd warning: forceEqualTipHeights.Rd:26: missing link ‘is.ultrametric’
  Rd warning: forceEqualTipHeights.Rd:31: missing link ‘chronos’
  Rd warning: index2DNAbin.Rd:10: missing link ‘DNAbin’
  Rd warning: ips-package.Rd:18: missing link ‘ladderize’
  Rd warning: ips-package.Rd:18: missing link ‘rotate’
  Rd warning: ips.16S.Rd:10: missing link ‘DNAbin’
  Rd warning: ips.28S.Rd:12: missing link ‘DNAbin’
  Rd warning: ips.cox1.Rd:12: missing link ‘DNAbin’
  Rd warning: mafft.Rd:53: missing link ‘phylo’
  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’
  Rd warning: mrbayes.Rd:22: missing link ‘DNAbin’
  Rd warning: multistate.Rd:63: missing link ‘ace’
  Rd warning: neighboringPairs.Rd:10: missing link ‘mst’
  Rd warning: ntip.Rd:10: missing link ‘phylo’
  Rd warning: pathd8.Rd:10: missing link ‘phylo’
  Rd warning: pathd8.Rd:22: missing link ‘phylo’
  Rd warning: phylo2mafft.Rd:10: missing link ‘phylo’
  Rd warning: phylo2mst.Rd:10: missing link ‘phylo’
  Rd warning: pis.Rd:10: missing link ‘DNAbin’
  Rd warning: raxml.Rd:26: missing link ‘DNAbin’
  Rd warning: raxml.Rd:57: missing link ‘phylo’
  Rd warning: raxml.partitions.Rd:11: missing link ‘DNAbin’
  Rd warning: raxml.partitions.Rd:23: missing link ‘cbind.DNAbin’
  Rd warning: rbeauti.Rd:22: missing link ‘DNAbin’
  Rd warning: read.Rd:56: missing link ‘cbind.DNAbin’
  Rd warning: sister.Rd:10: missing link ‘phylo’
  Rd warning: splitIntoClades.Rd:10: missing link ‘phylo’
  Rd warning: terminalSisters.Rd:10: missing link ‘phylo’
  Rd warning: tipHeights.Rd:13: missing link ‘phylo’
  Rd warning: tipHeights.Rd:23: missing link ‘branching.times’
  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’
  Rd warning: write.fas.Rd:26: missing link ‘DNAbin’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ips.Rcheck/00install.out’ for details.