Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/allocate_regimes_from_shifts.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/allocate_shifts_from_regimes.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/check_data.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/compute_betas_from_shifts.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/compute_dist_phy.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/compute_dist_phy.Rd:22: file link ‘dist.nodes’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/compute_shifts_from_betas.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/compute_times_ca.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/compute_times_ca.Rd:22: file link ‘node.depth.edgelength’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/enumerate_parsimony.Rd:11: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/enumerate_tips_under_edges.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/enumerate_tips_under_edges.Rd:20: file link ‘prop.part’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/equivalent_shifts.Rd:16: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/equivalent_shifts_edges.Rd:14: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/equivalent_shifts_values.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/incidence.matrix.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/incidence.matrix.full.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/init.alpha.gamma.estimation.Rd:27: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/init.parsimonyCost.Rd:12: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/log_likelihood.Rd:26: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/params_BM.Rd:54: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/params_OU.Rd:69: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/parsimonyCost.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/parsimonyNumber.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/partitionsNumber.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/shifts_to_simmap.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/simul_process.Rd:37: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/simulate_internal.Rd:26: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt8vHJ3/R.INSTALL26602b38ab6f/PhylogeneticEM/man/transform_branch_length.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PhylogeneticEM.Rcheck/00install.out’ for details.