• using R Under development (unstable) (2024-11-15 r87338)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.3 (2)     Debian flang-new version 19.1.3 (2)
• running under: Debian GNU/Linux trixie/sid
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘phytools’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [3s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
• checking loading without being on the library search path ... [3s/3s] 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 ... [139s/163s] OK
• checking Rd files ... [2s/2s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 ... [3s/3s] OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [48s/54s] OK Examples with CPU (user + system) or elapsed time > 5s            user system elapsed anc.Bayes 5.067 0.145 5.641
• checking PDF version of manual ... [15s/19s] OK
• checking HTML version of manual ... [11s/18s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE