* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/betapart.Rcheck’
* using R Under development (unstable) (2024-04-27 r86487)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.4 (1)
    Debian flang-new version 18.1.4 (1)
* 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-clang/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 ... [3s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/4s] 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 ... [25s/33s] OK
* checking Rd files ... [1s/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 Martínez-Santalla, Ramiro Martín-Devasa, Carola Gómez-Rodríguez, 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking examples ... [18s/27s] OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
zdep 5.861  0.018   6.331
* checking PDF version of manual ... [8s/11s] OK
* checking HTML version of manual ... [2s/4s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE