• using R version 2.14.2 RC (2012-02-23 r58468)
  • using platform: i686-pc-linux-gnu (32-bit)
  • using session charset: UTF-8
  • checking for file ‘phytools/DESCRIPTION’ ... OK
  • this is package ‘phytools’ version ‘0.1-6’
  • 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 whether package ‘phytools’ can be installed ... OK
  • checking installed package size ... OK
  • checking package directory ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking DESCRIPTION meta-information ... OK
  • checking top-level files ... OK
  • checking index information ... OK
  • checking package subdirectories ... OK
  • checking R files for non-ASCII characters ... OK
  • checking R files for syntax errors ... OK
  • checking whether the package can be loaded ... OK
  • checking whether the package can be loaded with stated dependencies ... OK
  • checking whether the package can be unloaded cleanly ... OK
  • checking whether the namespace can be loaded with stated dependencies ... OK
  • checking whether the namespace can be unloaded cleanly ... OK
  • checking for unstated 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 ... NOTE
    anc.Bayes: warning in determinant(C, log = T): partial argument match
    of 'log' to 'logarithm'
    anc.ML: warning in determinant(C, log = T): partial argument match of
    'log' to 'logarithm'
    mcmcBM: warning in determinant(C, log = T): partial argument match of
    'log' to 'logarithm'
    mcmcBM.full: warning in determinant(C, log = T): partial argument match
    of 'log' to 'logarithm'
    mcmcLambda: warning in determinant(C, log = T): partial argument match
    of 'log' to 'logarithm'
    mcmcLambda: warning in determinant(C.prime, log = T): partial argument
    match of 'log' to 'logarithm'
  • checking Rd files ... NOTE
    prepare_Rd: add.everywhere.Rd:15-16: Dropping empty section \details
    prepare_Rd: add.everywhere.Rd:22-23: Dropping empty section \references
    prepare_Rd: add.everywhere.Rd:28-29: Dropping empty section \examples
    prepare_Rd: allFurcTrees.Rd:30-31: Dropping empty section \examples
    prepare_Rd: anc.Bayes.Rd:16-17: Dropping empty section \details
    prepare_Rd: anc.Bayes.Rd:21-22: Dropping empty section \references
    prepare_Rd: anc.ML.Rd:15-17: Dropping empty section \details
    prepare_Rd: anc.ML.Rd:25-26: Dropping empty section \references
    prepare_Rd: anc.trend.Rd:26-27: Dropping empty section \references
    prepare_Rd: branching.diffusion.Rd:20-21: Dropping empty section \details
    prepare_Rd: branching.diffusion.Rd:25-26: Dropping empty section \references
    prepare_Rd: branching.diffusion.Rd:31-32: Dropping empty section \examples
    prepare_Rd: brownie.lite.Rd:19-20: Dropping empty section \details
    prepare_Rd: brownie.lite.Rd:49-50: Dropping empty section \examples
    prepare_Rd: brownieREML.Rd:15-16: Dropping empty section \details
    prepare_Rd: brownieREML.Rd:39-40: Dropping empty section \examples
    prepare_Rd: drop.clade.Rd:20-21: Dropping empty section \references
    prepare_Rd: drop.clade.Rd:23-24: Dropping empty section \seealso
    prepare_Rd: drop.clade.Rd:25-26: Dropping empty section \examples
    prepare_Rd: drop.tip.simmap.Rd:20-21: Dropping empty section \references
    prepare_Rd: drop.tip.simmap.Rd:26-27: Dropping empty section \examples
    prepare_Rd: estDiversity.Rd:27-28: Dropping empty section \examples
    prepare_Rd: evol.rate.mcmc.Rd:32-33: Dropping empty section \examples
    prepare_Rd: evol.vcv.Rd:39-40: Dropping empty section \examples
    prepare_Rd: evolvcv.lite.Rd:16-17: Dropping empty section \details
    prepare_Rd: evolvcv.lite.Rd:28-29: Dropping empty section \examples
    prepare_Rd: exhaustiveMP.Rd:30-31: Dropping empty section \examples
    prepare_Rd: expm.Rd:13-14: Dropping empty section \details
    prepare_Rd: expm.Rd:18-19: Dropping empty section \references
    prepare_Rd: expm.Rd:21-22: Dropping empty section \seealso
    prepare_Rd: expm.Rd:23-24: Dropping empty section \examples
    prepare_Rd: fastBM.Rd:19-20: Dropping empty section \details
    prepare_Rd: fastBM.Rd:24-25: Dropping empty section \references
    prepare_Rd: fastBM.Rd:30-31: Dropping empty section \examples
    prepare_Rd: fitBayes.Rd:18-19: Dropping empty section \details
    prepare_Rd: fitBayes.Rd:23-24: Dropping empty section \references
    prepare_Rd: fitBayes.Rd:29-30: Dropping empty section \examples
    prepare_Rd: fitDiversityModel.Rd:34-35: Dropping empty section \examples
    prepare_Rd: gammatest.Rd:25-26: Dropping empty section \seealso
    prepare_Rd: gammatest.Rd:27-28: Dropping empty section \examples
    prepare_Rd: lambda.transform.Rd:20-21: Dropping empty section \references
    prepare_Rd: lambda.transform.Rd:23-24: Dropping empty section \seealso
    prepare_Rd: lambda.transform.Rd:25-26: Dropping empty section \examples
    prepare_Rd: ls.tree.Rd:20-21: Dropping empty section \references
    prepare_Rd: ls.tree.Rd:23-24: Dropping empty section \seealso
    prepare_Rd: ls.tree.Rd:25-26: Dropping empty section \examples
    prepare_Rd: ltt.Rd:17-18: Dropping empty section \details
    prepare_Rd: make.era.map.Rd:14-15: Dropping empty section \details
    prepare_Rd: make.era.map.Rd:29-30: Dropping empty section \examples
    prepare_Rd: make.simmap.Rd:35-36: Dropping empty section \examples
    prepare_Rd: map.overlap.Rd:15-16: Dropping empty section \details
    prepare_Rd: map.overlap.Rd:20-21: Dropping empty section \references
    prepare_Rd: map.overlap.Rd:26-27: Dropping empty section \examples
    prepare_Rd: minSplit.Rd:16-17: Dropping empty section \details
    prepare_Rd: minSplit.Rd:31-32: Dropping empty section \examples
    prepare_Rd: mrp.supertree.Rd:31-32: Dropping empty section \examples
    prepare_Rd: nodeHeights.Rd:13-14: Dropping empty section \details
    prepare_Rd: nodeHeights.Rd:18-19: Dropping empty section \references
    prepare_Rd: optim.phylo.ls.Rd:37-38: Dropping empty section \examples
    prepare_Rd: paste.tree.Rd:20-21: Dropping empty section \references
    prepare_Rd: paste.tree.Rd:23-24: Dropping empty section \seealso
    prepare_Rd: pbtree.Rd:17-18: Dropping empty section \details
    prepare_Rd: pbtree.Rd:22-23: Dropping empty section \references
    prepare_Rd: pbtree.Rd:25-26: Dropping empty section \seealso
    prepare_Rd: pbtree.Rd:27-28: Dropping empty section \examples
    prepare_Rd: phenogram.Rd:17-18: Dropping empty section \details
    prepare_Rd: phenogram.Rd:22-24: Dropping empty section \references
    prepare_Rd: phenogram.Rd:26-27: Dropping empty section \seealso
    prepare_Rd: phyl.RMA.Rd:29-30: Dropping empty section \references
    prepare_Rd: phyl.RMA.Rd:35-36: Dropping empty section \examples
    prepare_Rd: phyl.cca.Rd:37-38: Dropping empty section \examples
    prepare_Rd: phyl.pairedttest.Rd:39-40: Dropping empty section \seealso
    prepare_Rd: phyl.pairedttest.Rd:41-42: Dropping empty section \examples
    prepare_Rd: phyl.pca.Rd:37-38: Dropping empty section \examples
    prepare_Rd: phyl.resid.Rd:36-37: Dropping empty section \examples
    prepare_Rd: phyl.vcv.Rd:21-22: Dropping empty section \references
    prepare_Rd: phyl.vcv.Rd:24-25: Dropping empty section \seealso
    prepare_Rd: phyl.vcv.Rd:26-27: Dropping empty section \examples
    prepare_Rd: phylANOVA.Rd:35-36: Dropping empty section \examples
    prepare_Rd: phyloDesign.Rd:19-20: Dropping empty section \references
    prepare_Rd: phyloDesign.Rd:22-23: Dropping empty section \seealso
    prepare_Rd: phyloDesign.Rd:24-25: Dropping empty section \examples
    prepare_Rd: phylomorphospace.Rd:17-18: Dropping empty section \details
    prepare_Rd: phylomorphospace.Rd:28-29: Dropping empty section \seealso
    prepare_Rd: phylomorphospace.Rd:30-31: Dropping empty section \examples
    prepare_Rd: phylosig.Rd:43-44: Dropping empty section \seealso
    prepare_Rd: plotSimmap.Rd:18-19: Dropping empty section \details
    prepare_Rd: plotTree.Rd:18-19: Dropping empty section \details
    prepare_Rd: plotTree.Rd:23-24: Dropping empty section \references
    prepare_Rd: posterior.evolrate.Rd:17-18: Dropping empty section \details
    prepare_Rd: posterior.evolrate.Rd:30-31: Dropping empty section \examples
    prepare_Rd: read.newick.Rd:20-21: Dropping empty section \references
    prepare_Rd: reorderSimmap.Rd:14-15: Dropping empty section \details
    prepare_Rd: reorderSimmap.Rd:19-20: Dropping empty section \references
    prepare_Rd: reorderSimmap.Rd:25-26: Dropping empty section \examples
    prepare_Rd: reroot.Rd:28-29: Dropping empty section \examples
    prepare_Rd: rstate.Rd:19-20: Dropping empty section \references
    prepare_Rd: rstate.Rd:22-23: Dropping empty section \seealso
    prepare_Rd: rstate.Rd:24-25: Dropping empty section \examples
    prepare_Rd: sampleFrom.Rd:17-18: Dropping empty section \details
    prepare_Rd: sampleFrom.Rd:22-24: Dropping empty section \references
    prepare_Rd: sampleFrom.Rd:26-27: Dropping empty section \seealso
    prepare_Rd: sampleFrom.Rd:28-30: Dropping empty section \examples
    prepare_Rd: sim.history.Rd:16-17: Dropping empty section \details
    prepare_Rd: sim.history.Rd:25-27: Dropping empty section \references
    prepare_Rd: sim.history.Rd:32-33: Dropping empty section \examples
    prepare_Rd: sim.rates.Rd:18-19: Dropping empty section \details
    prepare_Rd: sim.rates.Rd:23-24: Dropping empty section \references
    prepare_Rd: sim.rates.Rd:29-30: Dropping empty section \examples
    prepare_Rd: splitTree.Rd:20-21: Dropping empty section \references
    prepare_Rd: splitTree.Rd:23-24: Dropping empty section \seealso
    prepare_Rd: splitTree.Rd:25-26: Dropping empty section \examples
    prepare_Rd: starTree.Rd:20-21: Dropping empty section \references
    prepare_Rd: starTree.Rd:26-27: Dropping empty section \examples
    prepare_Rd: treeSlice.Rd:14-15: Dropping empty section \details
    prepare_Rd: treeSlice.Rd:19-20: Dropping empty section \references
    prepare_Rd: treeSlice.Rd:25-26: Dropping empty section \examples
    prepare_Rd: vcvPhylo.Rd:14-15: Dropping empty section \details
    prepare_Rd: vcvPhylo.Rd:19-20: Dropping empty section \references
    prepare_Rd: vcvPhylo.Rd:22-23: Dropping empty section \seealso
    prepare_Rd: vcvPhylo.Rd:24-25: Dropping empty section \examples
    prepare_Rd: write.simmap.Rd:16-17: Dropping empty section \details
    prepare_Rd: write.simmap.Rd:30-31: Dropping empty section \examples
  • checking Rd metadata ... OK
  • checking Rd cross-references ... OK
  • 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 examples ... OK
  • checking PDF version of manual ... OK