* using log directory ‘/srv/hornik/tmp/CRAN_pretest/Claddis.Rcheck’
* using R Under development (unstable) (2024-08-31 r87082)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘Claddis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Claddis’ version ‘0.7.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/6s] NOTE
Maintainer: ‘Graeme T. Lloyd <graemetlloyd@gmail.com>’

Possibly misspelled words in DESCRIPTION:
  Swofford (47:37)
  doi (47:69)

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following (possibly) invalid URLs:
  URL: https://travis-ci.com/graemetlloyd/Claddis (moved to https://www.travis-ci.com/graemetlloyd/Claddis)
    From: README.md
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* 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 ‘Claddis’ can be installed ... [9s/9s] OK
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [18s/18s] NOTE
calculate_gmax: possible error in ceiling(z = n_taxa/2): unused
  argument (z = n_taxa/2)
estimate_squared_change_ancestors: no visible global function
  definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
* checking Rd files ... [1s/1s] NOTE
checkRd: (-1) calculate_tree_length.Rd:78: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) calculate_tree_length.Rd:79: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) calculate_tree_length.Rd:80: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) calculate_tree_length.Rd:81: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) convert_adjacency_matrix_to_costmatrix.Rd:75: Lost braces
    75 | \link{convert_state_tree_to_adjacency_matrix}, link{locate_bracket_positions}
       |                                                    ^
checkRd: (-1) permute_all_treeshape_labellings.Rd:10: Lost braces
    10 | \item{treeshapes}{A vector of treeshape(s) in the same format as link{permute_treeshapes}.}
       |                                                                      ^
checkRd: (-1) permute_all_treeshape_labellings.Rd:25: Lost braces
    25 | Here treeshapes are encoded in the same pseudo-Newick format as the link{permute_treeshapes} function, e.g.:
       |                                                                         ^
* 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:
  drop_time_tip.Rd: drop.tip, ape
  estimate_ancestral_states.Rd: rerootingMethod, phytools, ace, ape
  find_minimum_spanning_edges.Rd: mst, ape
  find_unique_trees.Rd: unique.multiPhylo
  fix_root_time.Rd: drop.tip, ape
  ordinate_cladistic_matrix.Rd: pcoa, ape
  permute_tipstates.Rd: 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/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [16s/16s] OK
* checking PDF version of manual ... [7s/6s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character   (U+2009)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘Claddis-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 5 NOTEs