* using log directory 'd:/Rcompile/CRANpkg/local/4.5/phytools.Rcheck'
* using R Under development (unstable) (2024-07-14 r86899 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'phytools/DESCRIPTION' ... OK
* this is package 'phytools' version '2.3-0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'phytools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s] OK
* checking whether the package can be unloaded cleanly ... [2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s] OK
* checking loading without being on the library search path ... [2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [75s] OK
* checking Rd files ... [4s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add.arrow.Rd: nodelabels
  add.random.Rd: plot.phylo
  anc.Bayes.Rd: ace
  anc.ML.Rd: ace
  anc.trend.Rd: ace
  ancr.Rd: nodelabels
  bd.Rd: birthdeath
  bind.tip.Rd: bind.tree
  bind.tree.simmap.Rd: bind.tree
  cladelabels.Rd: nodelabels
  cophylo.Rd: cophyloplot
  describe.simmap.Rd: all.equal.phylo
  di2multi.simmap.Rd: di2multi, multi2di
  drop.tip.contMap.Rd: drop.tip, keep.tip
  drop.tip.multiSimmap.Rd: drop.tip, keep.tip, drop.tip.multiPhylo
  drop.tip.simmap.Rd: drop.tip, keep.tip, extract.clade
  estDiversity.Rd: ace
  exhaustiveMP.Rd: phyDat, parsimony, optim.parsimony, pratchet
  export.as.xml.Rd: read.nexus
  fancyTree.Rd: drop.tip, plot.phylo
  fastAnc.Rd: ace, pic
  fastMRCA.Rd: getMRCA, mrca
  findMRCA.Rd: mrca, vcv.phylo, getMRCA
  fit.bd.Rd: birthdeath
  fitMk.Rd: ace
  fitPagel.Rd: ace
  force.ultrametric.Rd: nnls.tree, is.ultrametric
  getCladesofSize.Rd: extract.clade
  getDescendants.Rd: Descendants
  getSisters.Rd: Siblings
  labelnodes.Rd: nodelabels
  ladderize.simmap.Rd: ladderize
  lambda.transform.Rd: vcv.phylo
  likMlambda.Rd: vcv.phylo
  linklabels.Rd: nodelabels, tiplabels
  make.simmap.Rd: ace
  map.to.singleton.Rd: plot.phylo, collapse.singles, drop.tip
  midpoint.root.Rd: midpoint, root
  modified.Grafen.Rd: compute.brlen
  mrp.supertree.Rd: pratchet, optim.parsimony, prop.part
  multiC.Rd: vcv.phylo
  multiRF.Rd: prop.part
  nodelabels.cophylo.Rd: nodelabels, edgelabels, tiplabels
  optim.phylo.ls.Rd: nni
  pbtree.Rd: bind.tree
  pgls.Ives.Rd: gls
  phyl.resid.Rd: gls
  phyl.vcv.Rd: vcv.phylo
  phylo.to.map.Rd: map
  phylomorphospace3d.Rd: scatterplot3d
  plotBranchbyTrait.Rd: plot.phylo
  plotSimmap.Rd: nodelabels, plot.phylo
  plotThresh.Rd: plot.phylo
  plotTree.Rd: plot.phylo
  ratebystate.Rd: pic
  ratebytree.Rd: ginv, ace
  read.newick.Rd: read.nexus, read.tree, collapse.singles
  read.simmap.Rd: read.nexus, read.tree
  reorder.backbonePhylo.Rd: reorder.phylo
  reorderSimmap.Rd: reorder.phylo
  rep.phylo.Rd: c.phylo
  reroot.Rd: root
  rerootingMethod.Rd: ace
  resolveNode.Rd: multi2di
  rotateNodes.Rd: rotate
  starTree.Rd: stree
  treeSlice.Rd: extract.clade
  untangle.Rd: plot.phylo, reorder.phylo, read.tree
  vcvPhylo.Rd: vcv.phylo
  writeAncestors.Rd: ace, write.tree
  writeNexus.Rd: write.nexus
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [2s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [50s] OK
* checking PDF version of manual ... [32s] OK
* checking HTML version of manual ... [35s] OK
* DONE
Status: 1 NOTE