• using R Under development (unstable) (2023-11-30 r85651)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-13 (Debian 13.2.0-5) 13.2.0     GNU Fortran (Debian 13.2.0-5) 13.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘geomorph/DESCRIPTION’ ... OK
• this is package ‘geomorph’ version ‘4.0.6’
• package encoding: UTF-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 ‘geomorph’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 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/5s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/6s] OK
• checking loading without being on the library search path ... [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 ... [48s/79s] OK
• checking Rd files ... [1s/2s] NOTE checkRd: (-1) bilat.symmetry.Rd:40: Lost braces; missing escapes or markup?     40 | symmetry {=TRUE} or matching symmetry {=FALSE}}        | ^ checkRd: (-1) bilat.symmetry.Rd:40: Lost braces; missing escapes or markup?     40 | symmetry {=TRUE} or matching symmetry {=FALSE}}        | ^ checkRd: (-1) bilat.symmetry.Rd:128: Lost braces; missing escapes or markup?    128 | Analyses of symmetry for matched pairs of objects is implemented when {object.sym=FALSE}. Here,        | ^ checkRd: (-1) bilat.symmetry.Rd:139: Lost braces; missing escapes or markup?    139 | Analyses of object symmetry is implemented when {object.sym=TRUE}. Here, a 3D array [p x k x n]        | ^ checkRd: (-1) compare.evol.rates.Rd:20: Lost braces; missing escapes or markup?     20 | \item{phy}{A phylogenetic tree of {class phylo} - see \code{\link[ape]{read.tree}} in library ape}        | ^ checkRd: (-1) compare.multi.evol.rates.Rd:22: Lost braces; missing escapes or markup?     22 | \item{phy}{A phylogenetic tree of {class phylo} - see \code{\link[ape]{read.tree}} in library ape}        | ^ checkRd: (-1) gm.prcomp.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:59-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:61-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:65-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:74: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:75: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:77-78: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:91-92: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:93-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:96-100: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:101-104: Lost braces in \itemize; meant \describe ? checkRd: (-1) gm.prcomp.Rd:197: Lost braces    197 | \code{\link{ordinate}}{ A more bare-bones ordination function on which gm.prcomp depends.}        | ^ checkRd: (-1) integration.Vrel.Rd:12: Lost braces; missing escapes or markup?     12 | \item{phy}{A phylogenetic tree of {class phylo} - see \code{\link[ape]{read.tree}} in library ape}        | ^ checkRd: (-1) phylo.integration.Rd:22: Lost braces; missing escapes or markup?     22 | \item{phy}{A phylogenetic tree of {class phylo} - see \code{\link[ape]{read.tree}} in library ape}        | ^ checkRd: (-1) phylo.modularity.Rd:23: Lost braces; missing escapes or markup?     23 | \item{phy}{A phylogenetic tree of {class phylo} - see \code{\link[ape]{read.tree}} in library ape}        | ^ checkRd: (-1) physignal.Rd:12: Lost braces; missing escapes or markup?     12 | \item{phy}{A phylogenetic tree of {class phylo} - see \code{\link[ape]{read.tree}} in library ape}        | ^ checkRd: (-1) physignal.z.Rd:22: Lost braces; missing escapes or markup?     22 | \item{phy}{A phylogenetic tree of {class phylo} - see \code{\link[ape]{read.tree}} in library ape}        | ^ checkRd: (-1) physignal.z.Rd:113-118: Lost braces in \itemize; meant \describe ? checkRd: (-1) physignal.z.Rd:119-122: Lost braces in \itemize; meant \describe ? checkRd: (-1) physignal.z.Rd:123-129: Lost braces in \itemize; meant \describe ? checkRd: (-1) physignal.z.Rd:130-132: Lost braces in \itemize; meant \describe ? checkRd: (-1) physignal.z.Rd:133-135: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotRefToTarget.Rd:27: Lost braces; missing escapes or markup?     27 | \item{mesh}{A mesh3d object for use with {method="surface"}}        | ^ checkRd: (-1) plotRefToTarget.Rd:43: Lost braces; missing escapes or markup?     43 | \item{useRefPts}{An option (logical value) to use reference configuration points rather than target configuration points (when {method = "TPS"})}        | ^ checkRd: (-1) plotRefToTarget.Rd:55: Lost braces; missing escapes or markup?     55 | specimen. The option {mag} allows the user to indicates the degree of magnification to be used when        | ^ checkRd: (-1) plotRefToTarget.Rd:78: Lost braces; missing escapes or markup?     78 | Requires mesh3d object in option {mesh}, made using \code{\link{warpRefMesh}}.        | ^ checkRd: (-1) plotRefToTarget.Rd:48: Lost braces; missing escapes or markup?     48 | If using {method="surface"}, function will return the warped mesh3d object.        | ^ checkRd: (-1) plotspec.Rd:23: Lost braces; missing escapes or markup?     23 | \item{fixed}{Numeric The number of fixed template landmarks (listed first in {digitspec})}        | ^ checkRd: (-1) plotspec.Rd:31: Lost braces; missing escapes or markup?     31 | \item{centered}{Logical Whether the data matrix is in the surface mesh coordinate system ({centered = FALSE}) or        | ^ checkRd: (-1) plotspec.Rd:32: Lost braces; missing escapes or markup?     32 | if the data were collected after the mesh was centered ({centered = TRUE})- see details.}        | ^ checkRd: (-1) plotspec.Rd:45: Lost braces; missing escapes or markup?     45 | Therefore use this function with {centered=TRUE}. Data collected outside geomorph should be read using        | ^ checkRd: (-1) plotspec.Rd:46: Lost braces; missing escapes or markup?     46 | {centered=FALSE}. The function assumes the fixed landmarks are listed at the beginning of        | ^ checkRd: (-1) plotspec.Rd:47: Lost braces; missing escapes or markup?     47 | the coordinate matrix ({digitspec}).        | ^ checkRd: (-1) procD.pgls.Rd:25: Lost braces; missing escapes or markup?     25 | \item{phy}{A phylogenetic tree of {class phylo} - see \code{\link[ape]{read.tree}} in library ape}        | ^
• 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 ... [0s/1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [13s/22s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking re-building of vignette outputs ... [101s/165s] OK
• checking PDF version of manual ... [12s/25s] OK
• checking HTML version of manual ... [5s/12s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE