• using R Under development (unstable) (2024-12-20 r87452)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (GCC) 14.2.0     GNU Fortran (GCC) 14.2.0
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 ... OK See the install log for details.
• 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ade4’   All declared Imports should be used.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [12s/15s] OK
• checking Rd files ... 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 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [9s/11s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [66s/84s] OK
• checking PDF version of manual ... [9s/16s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 NOTEs