* using log directory ‘/srv/hornik/tmp/CRAN/RPANDA.Rcheck’
* using R Under development (unstable) (2024-02-04 r85859)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘RPANDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RPANDA’ version ‘2.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/7s] NOTE
Maintainer: ‘Hélène Morlon <helene.morlon@bio.ens.psl.eu>’

Possibly misspelled words in DESCRIPTION:
  Mazet (47:123)

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.
* 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 ‘RPANDA’ can be installed ... [37s/37s] OK
* used C compiler: ‘Debian clang version 17.0.6 (5)’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Mismatches for apparent methods not registered:
plot:
  function(x, ...)
plot.with.trait:
  function(phylo, rate, scale, lwd, direction)

plot:
  function(x, ...)
plot.network:
  function(link, spec, trait.id, method, order, scale)

plot:
  function(x, ...)
plot.species:
  function(spec, trait.id, net, ...)

mean:
  function(x, ...)
mean.rate:
  function(tree, rate)

abs:
  function(x)
abs.to.rel:
  function(tree, true.rate, lambda_0)
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [64s/64s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [7s/7s] 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 compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [56s/56s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [7s/7s] OK
  Running ‘test-all.R’ [7s/7s]
* checking PDF version of manual ... [6s/6s] OK
* checking HTML version of manual ... [3s/3s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs