Found the following significant warnings:
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/all.equal.DNAbin.Rd:25: file link ‘isTRUE’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/compar.gee.Rd:105: file link ‘drop1’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/image.DNAbin.Rd:40: file link ‘image.default’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/is.ultrametric.Rd:34: file link ‘.Machine’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/ltt.plot.Rd:110: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/mst.Rd:61: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/phydataplot.Rd:48: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/plot.correlogram.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/plot.phylo.Rd:194: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/plotTreeTime.Rd:26: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/reorder.phylo.Rd:62: file link ‘reorder’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/skylineplot.Rd:40: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/zoom.Rd:37: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/zoom.Rd:43: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKLWq9y/R.INSTALL5162545cebeb/ape/man/zoom.Rd:44: file link ‘grey’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ape.Rcheck/00install.out’ for details.