* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/betapart.Rcheck’ * using R Under development (unstable) (2025-02-26 r87830) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-16) 14.2.0 GNU Fortran (Debian 14.2.0-16) 14.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘betapart/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘betapart’ version ‘1.6’ * 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 serialization versions ... OK * checking whether package ‘betapart’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/betapart-00install.html' for details. * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s/3s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [1s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/3s] 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 ... [13s/22s] OK * checking Rd files ... [0s/1s] NOTE checkRd: (-1) beta.pair.Rd:46: Lost braces 46 | \code{\link{beta.pair.abund}}, code{\link{beta.multi}}, \code{\link{beta.sample}}, \code{\link{betapart.core}}, \code{\link{beta.temp}} | ^ checkRd: (-1) betapart-package.Rd:36: Lost braces; missing escapes or markup? 36 | Andres Baselga, David Orme, Sebastien Villéger, Julien {De Bortoli}, Fabien Leprieur, Maxime Logez, Sara MartÃnez-Santalla, Ramiro MartÃn-Devasa, Carola Gómez-RodrÃguez, and Rosa M. Crujeiras | ^ checkRd: (-1) decay.model.Rd:22: Lost braces 22 | \item{y}{ code{dist} object, either containing similarities or dissimilarities between pairs of assemblages.} | ^ checkRd: (-1) decay.model.Rd:23: Lost braces 23 | \item{x}{ code{dist} object, containing distances (spatial or other) between pairs of assemblages.} | ^ checkRd: (-1) decay.model.Rd:26: Lost braces 26 | \item{y.type}{ polarity of the code{dist} object (i.e. 1 means total similarity or total dissimilarity), | ^ checkRd: (-1) decay.model.Rd:35: Lost braces 35 | \item{data.y}{ original y data, code{dist} object, either containing similarities or dissimilarities between pairs of assemblages.} | ^ checkRd: (-1) decay.model.Rd:36: Lost braces 36 | \item{data.x}{ original x data, code{dist} object, containing distances (spatial or other) between pairs of assemblages.} | ^ checkRd: (-1) functional.betapart.core.pairwise.Rd:63-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) functional.betapart.core.pairwise.Rd:68-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) functional.betapart.core.pairwise.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) functional.betapart.core.pairwise.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: functional.betapart.core.Rd: convhulln functional.betapart.core.pairwise.Rd: convhulln inter_geom.Rd: intersectn qhull.opt.Rd: convhulln Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 data for ASCII and uncompressed saves ... OK * checking examples ... [8s/15s] OK * checking PDF version of manual ... [4s/6s] OK * checking HTML version of manual ... [1s/2s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 2 NOTEs