* using log directory 'd:/Rcompile/CRANpkg/local/4.5/TreeSearch.Rcheck'
* using R Under development (unstable) (2024-11-07 r87302 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'TreeSearch/DESCRIPTION' ... OK
* this is package 'TreeSearch' version '1.5.1'
* package encoding: UTF-8
* 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 'TreeSearch' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
* checking C++ specification ... OK
* checking installed package size ... INFO
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
* checking package directory ... OK
* checking 'build' 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 ... [12s] OK
* checking Rd files ... [6s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AdditionTree.Rd: ImposeConstraint
  AllSPR.Rd: phylo
  CharacterLength.Rd: phylo
  ConcordantInformation.Rd: phylo
  Consistency.Rd: phylo
  DoubleNNI.Rd: phylo
  JackLabels.Rd: phylo
  Jackknife.Rd: phylo
  MaximizeParsimony.Rd: phylo, ImposeConstraint
  MorphyTreeLength.Rd: RenumberTips, phylo
  NNI.Rd: phylo
  PlotCharacter.Rd: phylo
  Ratchet.Rd: phylo
  RearrangeEdges.Rd: phylo
  SPR.Rd: phylo
  SiteConcordance.Rd: phylo
  StopUnlessBifurcating.Rd: phylo
  SuccessiveApproximations.Rd: phylo
  TBR.Rd: phylo
  TBRWarning.Rd: phylo
  TaxonInfluence.Rd: ClusteringInfoDistance, write.nexus, path_sanitize
  TreeSearch.Rd: phylo
  cSPR.Rd: phylo
  dot-NonDuplicateRoot.Rd: phylo
  inapplicable.datasets.Rd: read.nexus.data
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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [16s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [62s] OK
  Running 'spelling.R' [0s]
  Running 'testthat.R' [61s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [86s] OK
* checking PDF version of manual ... [28s] OK
* checking HTML version of manual ... [15s] OK
* DONE
Status: 1 NOTE