• using R version 4.5.0 beta (2025-03-29 r88069)
  • using platform: aarch64-apple-darwin20
  • R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
  • running under: macOS Ventura 13.4
  • using session charset: UTF-8
  • checking for file ‘PBD/DESCRIPTION’ ... OK
  • checking extension type ... Package
  • this is package ‘PBD’ version ‘1.4’
  • 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 ‘PBD’ can be installed ... [1s/2s] OK See the install log for details.
  • checking installed package size ... OK
  • 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 ... [0s/0s] OK
  • checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
  • checking whether the package can be unloaded cleanly ... [0s/0s] OK
  • checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
  • checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
  • checking loading without being on the library search path ... [0s/0s] 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 ... [2s/2s] OK
  • checking Rd files ... [0s/0s] NOTE checkRd: (-1) pbd_loglik.Rd:31: Lost braces     31 | \code{pars2[1]} {set the conditioning on non-extinction of the clade (1) or not (0) \cr \cr}        | ^ checkRd: (-1) pbd_loglik.Rd:32: Lost braces     32 | \code{pars2[2]} {sets whether the likelihood is for the branching times (0) or the phylogeny (1) \cr \cr}        | ^ checkRd: (-1) pbd_loglik.Rd:33: Lost braces     33 | \code{pars2[3]} {sets whether the first element of the branching times is the stem (1) or the crown (2) age \cr \cr}        | ^ checkRd: (-1) pbd_loglik.Rd:34: Lost braces     34 | \code{pars2[4]} {sets whether the parameters and likelihood should be shown on screen (1) or not (0) \cr \cr}        | ^ checkRd: (-1) pbd_loglik.Rd:35: Lost braces     35 | \code{pars2[5]} {sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details. \cr \cr}        | ^ checkRd: (-1) pbd_loglik.Rd:36: Lost braces     36 | \code{pars2[6]}{Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}        | ^ checkRd: (-1) pbd_loglik.Rd:37: Lost braces     37 | \code{pars2[7]}{Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}        | ^
  • 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 installed files from ‘inst/doc’ ... OK
  • checking files in ‘vignettes’ ... OK
  • checking examples ... [2s/2s] OK
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes ... OK
  • checking re-building of vignette outputs ... [19s/26s] OK
  • checking PDF version of manual ... [5s/6s] OK
  • DONE Status: 1 NOTE
  • using check arguments '--no-clean-on-error '