* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘phytools’ ...
** package ‘phytools’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘phytools’
finding HTML links ... done
Dtest html
add.arrow html
add.color.bar html
add.everywhere html
add.random html
add.simmap.legend html
add.species.to.genus html
aic.w html
allFurcTrees html
anc.Bayes html
anc.ML html
anc.trend html
ancThresh html
ancr html
anoletree html
ansi_phylo html
applyBranchLengths html
as.Qmatrix html
as.multiPhylo html
ave.rates html
averageTree html
bd html
bind.tip html
bind.tree.simmap html
bmPlot html
bounded_bm html
branching.diffusion html
brownie.lite html
brownieREML html
cladelabels html
collapse.to.star html
collapseTree html
compare.chronograms html
consensus.edges html
contMap html
cophylo html
cospeciation html
countSimmap html
ctt html
density.multiSimmap html
densityMap html
densityTree html
describe.simmap html
di2multi.simmap html
dotTree html
drop.clade html
drop.leaves html
drop.tip.contMap html
drop.tip.multiSimmap html
drop.tip.simmap html
edge.widthMap html
edgeProbs html
estDiversity html
evol.rate.mcmc html
evol.vcv html
evolvcv.lite html
exhaustiveMP html
expand.clade html
export.as.xml html
fancyTree html
fastAnc html
fastBM html
fastMRCA html
findMRCA html
fit.bd html
fitBayes html
fitDiversityModel html
fitMk html
fitPagel html
fitThresh html
fitmultiBM html
force.ultrametric html
gamma_pruning html
gammatest html
genSeq html
geo.legend html
get.treepos html
getCladesofSize html
getDescendants html
getExtant html
getSisters html
getStates html
labelnodes html
ladderize.simmap html
lambda.transform html
likMlambda html
linklabels html
locate.fossil html
locate.yeti html
ls.tree html
ltt html
ltt95 html
make.era.map html
make.simmap html
map.overlap html
map.to.singleton html
mapped.states html
markChanges html
matchNodes html
mergeMappedStates html
midpoint.root html
minRotate html
minSplit html
modified.Grafen html
mrp.supertree html
multi.mantel html
multiC html
multiRF html
multirateBM html
nodeHeights html
nodelabels.cophylo html
optim.phylo.ls html
orderMappedEdge html
paintSubTree html
paste.tree html
pbtree html
pgls.Ives html
phenogram html
phyl.RMA html
phyl.cca html
phyl.pairedttest html
phyl.pca html
phyl.resid html
phyl.vcv html
phylANOVA html
phylo.heatmap html
phylo.impute html
phylo.to.map html
phylo.toBackbone html
phyloDesign html
phylomorphospace html
phylomorphospace3d html
phylosig html
phytools-package html
plot.backbonePhylo html
plotBranchbyTrait html
plotSimmap html
plotThresh html
plotTree html
plotTree.datamatrix html
plotTree.errorbars html
plotTree.lollipop html
plotTree.wBars html
posterior.evolrate html
posthoc html
print.backbonePhylo html
pscore html
ratebystate html
ratebytree html
rateshift html
read.newick html
read.simmap html
reorder.backbonePhylo html
reorderSimmap html
rep.phylo html
reroot html
rerootingMethod html
rescale html
rescaleSimmap html
resolveNode html
rotateNodes html
roundBranches html
roundPhylogram html
rstate html
sampleFrom html
setMap html
sim.corrs html
sim.history html
sim.ratebystate html
sim.rates html
simBMphylo html
skewers html
splitEdgeColor html
splitTree html
splitplotTree html
starTree html
strahlerNumber html
threshBayes html
threshDIC html
threshState html
to.matrix html
tree.grow html
treeSlice html
untangle html
vcvPhylo html
write.simmap html
writeAncestors html
writeNexus html
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (phytools)