Found the following significant warnings:
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/MOStest.Rd:150: file link ‘confint.glm’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/cascadeKM.Rd:36: file link ‘clustIndex’ in package ‘cclust’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/cascadeKM.Rd:65: file link ‘clustIndex’ in package ‘cclust’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/cascadeKM.Rd:179: file link ‘clustIndex’ in package ‘cclust’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/goodness.metaMDS.Rd:12: file link ‘Shepard’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/goodness.metaMDS.Rd:75: file link ‘Shepard’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/humpfit.Rd:87: file link ‘pairs.profile’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/humpfit.Rd:88: file link ‘confint.profile.glm’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/humpfit.Rd:147: file link ‘confint.glm’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/oecosimu.Rd:164: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/ordipointlabel.Rd:52: file link ‘pointLabel’ in package ‘maptools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/ordipointlabel.Rd:76: file link ‘pointLabel’ in package ‘maptools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/ordipointlabel.Rd:82: file link ‘pointLabel’ in package ‘maptools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/orditkplot.Rd:128: file link ‘tkcanvas’ in package ‘tcltk’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/ordixyplot.Rd:60: file link ‘trellis.par.set’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/ordixyplot.Rd:62: file link ‘panel.arrows’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/ordixyplot.Rd:66: file link ‘trellis.par.set’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/ordixyplot.Rd:102: file link ‘panel.splom’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/ordixyplot.Rd:126: file link ‘panel.splom’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/permustats.Rd:58: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/permustats.Rd:115: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/permustats.Rd:120: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/permustats.Rd:158: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/treedive.Rd:76: file link ‘as.hclust.phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/vegan-defunct.Rd:69: file link ‘nobs-methods’ in package ‘permute’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAkVIWt/R.INSTALL6e6926d81bd0/vegan/man/vegemite.Rd:131: file link ‘as.hclust.phylo’ 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/vegan.Rcheck/00install.out’ for details.