* using log directory 'd:/Rcompile/CRANpkg/local/4.5/Claddis.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 'Claddis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Claddis' version '0.6.3'
* 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 'Claddis' 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 ... [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 ... [17s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estimate_ancestral_states.Rd: rerootingMethod, phytools, ace, ape
  find_minimum_spanning_edges.Rd: mst, ape
  fix_root_time.Rd: drop.tip, ape
  map_stochastic_changes.Rd: make.simmap, phytools
  ordinate_cladistic_matrix.Rd: pcoa, ape
  plot_rates_character.Rd: geoscale
  plot_rates_time.Rd: geoscalePlot, geoscale
  plot_rates_tree.Rd: geoscale
  read_nexus_matrix.Rd: read.nexus.data
  safe_taxonomic_reinsertion.Rd: ape, read.tree, read.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 ... [0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [18s] OK
* checking PDF version of manual ... [23s] OK
* checking HTML version of manual ... [8s] OK
* DONE
Status: 1 NOTE