• using R version 4.5.0 beta (2025-03-29 r88074)
• using platform: x86_64-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 13.3.1
• using session charset: UTF-8
• checking for file ‘vhica/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘vhica’ version ‘0.2.8’
• 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 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 ‘vhica’ can be installed ... [2s/2s] OK See the install log for details.
• 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 ... [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 ... [3s/3s] OK
• checking Rd files ... [0s/0s] NOTE checkRd: (-1) div.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) div.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) div.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) image.vhica.Rd:74: Lost braces     74 | The function returns (invisibly) a list of elements (object of class \code{vhicaimage}) which can be used for further analysis: \code{tree} contains the phylogenetic tree (object of class \code{"phylo"}), \code{species} is the vector of species, \code{stats} is a matrix of log10(P-values) (positive elements are minus log10(P) corresponding to positive residuals), code{dS} is a matrix reminding the divergence rates from the data. Calling the method \code{\link{summary.vhicaimage}} on this object returns a nicely formatted data frame.        | ^ checkRd: (-1) read.vhica.Rd:59-74: Lost braces in \itemize; meant \describe ? checkRd: (-1) read.vhica.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) read.vhica.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) read.vhica.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) read.vhica.Rd:75-92: Lost braces in \itemize; meant \describe ? checkRd: (-1) read.vhica.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) read.vhica.Rd:88: Lost braces in \itemize; meant \describe ? checkRd: (-1) read.vhica.Rd:89: Lost braces in \itemize; meant \describe ? checkRd: (-1) read.vhica.Rd:90: Lost braces in \itemize; meant \describe ? checkRd: (-1) read.vhica.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) read.vhica.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) read.vhica.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) read.vhica.Rd:102: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) read.vhica.Rd:103: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) read.vhica.Rd:104: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) read.vhica.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) vhica-package.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) vhica-package.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) vhica-package.Rd:26: Lost braces in \itemize; meant \describe ?
• 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 examples ... [5s/4s] OK
• checking PDF version of manual ... [6s/8s] OK
• DONE Status: 1 NOTE
• using check arguments '--no-clean-on-error '