* using log directory 'd:/Rcompile/CRANpkg/local/4.4/vhica.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'vhica' can be installed ... OK
* 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] OK
* checking whether the package can be loaded with stated dependencies ... [0s] OK
* checking whether the package can be unloaded cleanly ... [0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s] OK
* checking loading without being on the library search path ... [0s] 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 ... [4s] OK
* checking Rd files ... [1s] 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 ... [4s] OK
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [2s] OK
* DONE
Status: 1 NOTE