• using R Under development (unstable) (2023-12-04 r85659)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-13 (Debian 13.2.0-7) 13.2.0     GNU Fortran (Debian 13.2.0-7) 13.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘dispRity/DESCRIPTION’ ... OK
• this is package ‘dispRity’ version ‘1.7.0’
• 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 ‘dispRity’ can be installed ... OK See the install log for details.
• used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
• 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 ... [3s/6s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the package can be unloaded cleanly ... [3s/4s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [3s/6s] OK
• checking whether startup messages can be suppressed ... [3s/5s] 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 ... [49s/78s] OK
• checking Rd files ... [1s/2s] NOTE checkRd: (-1) covar.plot.Rd:63: Lost braces     63 | \item code{"intercept"} for using the estimated posterior intercept for each sample.        | ^ checkRd: (-1) crown.stem.Rd:10: Lost braces     10 | \item{tree}{a code{"phylo"} object}        | ^ checkRd: (-1) dispRity.metric.Rd:46: Lost braces     46 | \item{...}{Optional arguments to be passed to the function. Usual optional arguments are \code{method} for specifying the method for calculating distance passed to \code{\link[vegan]{vegdist}} (e.g. \code{method = "euclidean"} - default - or \code{method = "manhattan"}) or \code{k.root} to scale the result using the eqn{kth} root. See details below for available optional arguments for each function.}        | ^ checkRd: (-1) dispRity.metric.Rd:79: Lost braces; missing escapes or markup?     79 | \item \code{func.div}: The functional divergence (Vill'{e}ger et al. 2008): the ratio of deviation from the centroid (this is similar to \code{FD::dbFD()$FDiv}).        | ^ checkRd: (-1) dispRity.metric.Rd:81: Lost braces; missing escapes or markup?     81 | \item \code{func.eve}: The functional evenness (Vill'{e}ger et al. 2008): the minimal spanning tree distances evenness (this is similar to \code{FD::dbFD()$FEve}). If the matrix used is not a distance matrix, the distance method can be passed using, for example \code{method = "euclidean"} (default).        | ^ checkRd: (-1) dispRity.metric.Rd:97: Lost braces; missing escapes or markup?     97 | \item \code{centroids}: calculates the distance between each row and the centroid of the matrix (Lalibert'{e} 2010). This function can take an optional arguments \code{centroid} for defining the centroid (if missing (default), the centroid of the matrix is used). This argument can be either a subset of coordinates matching the matrix's dimensions (e.g. \code{c(0, 1, 2)} for a matrix with three columns) or a single value to be the coordinates of the centroid (e.g. \code{centroid = 0} will set the centroid coordinates to \code{c(0, 0, 0)} for a three dimensional matrix). NOTE: distance is calculated as \code{"euclidean"} by default, this can be changed using the \code{method} argument.        | ^ checkRd: (-1) dispRity.metric.Rd:119: Lost braces    119 | Other options include the centering of the projections on 0.5 (code{centre = TRUE}; default) ranging the projection onto the vector (\code{point1}, \code{point2}) between -1 and 1 (higher or lower values project beyond the vector); and whether to output the projection values as absolute values (\code{abs = TRUE}; default). These two last options only affect the results from \code{measure = "position"}.        | ^ checkRd: (-1) dtt.dispRity.Rd:33: Lost braces     33 | \item{...}{Any other arguments to be passed to \\code{geiger::dtt}.}        | ^ checkRd: (-1) model.test.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) model.test.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) model.test.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) model.test.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) model.test.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) model.test.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) model.test.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) model.test.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) model.test.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) model.test.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) model.test.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
• 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 ... [3s/5s] 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 ... [30s/45s] OK Examples with CPU (user + system) or elapsed time > 5s              user system elapsed null.test 4.737 0.001 6.959 multi.ace 4.342 0.059 6.279 test.metric 3.181 0.028 5.359
• checking PDF version of manual ... [8s/17s] OK
• checking HTML version of manual ... [4s/10s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE