Found the following significant warnings:
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/as_phyloseq.Rd:40: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/as_phyloseq.Rd:45: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/heat_tree.Rd:381: file link ‘nicely’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/heat_tree.Rd:382: file link ‘as_tree’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/heat_tree.Rd:383: file link ‘with_dh’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/heat_tree.Rd:384: file link ‘with_gem’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/heat_tree.Rd:385: file link ‘with_graphopt’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/heat_tree.Rd:386: file link ‘with_mds’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/heat_tree.Rd:387: file link ‘with_fr’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/heat_tree.Rd:388: file link ‘with_kk’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/heat_tree.Rd:389: file link ‘with_lgl’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/heat_tree.Rd:390: file link ‘with_drl’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/layout_functions.Rd:36: file link ‘graph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/parse_rdp.Rd:16: file link ‘read.FASTA’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/parse_seq_input.Rd:21: file link ‘read.FASTA’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/parse_silva_fasta.Rd:19: file link ‘read.FASTA’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/parse_unite_general.Rd:16: file link ‘read.FASTA’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/primersearch_raw.Rd:16: file link ‘read.FASTA’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/rarefy_obs.Rd:54: file link ‘rrarefy’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2VToRF/R.INSTALL260c590105c6/metacoder/man/read_fasta.Rd:19: file link ‘read.FASTA’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/metacoder.Rcheck/00install.out’ for details.