* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/dendextend.Rcheck’ * using R Under development (unstable) (2024-04-27 r86487) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘dendextend/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dendextend’ version ‘1.17.1’ * 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 ‘dendextend’ can be installed ... [20s/47s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/dendextend-00install.html' for details. * checking package directory ... 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... [42s/95s] OK * checking Rd files ... NOTE checkRd: (-1) assign_values_to_leaves_edgePar.Rd:60: Lost braces 60 | \link{get_leaves_attr}, link{assign_values_to_leaves_nodePar} | ^ checkRd: (-1) khan.Rd:10-11: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:12-13: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:14-15: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:16-18: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:19-21: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:22-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) khan.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) ladderize.Rd:59: Lost braces; missing escapes or markup? 59 | \code{\link{rev.dendrogram}}, \code{\link{rotate}} ({dendextend}), \code{\link[ape]{rotate}} ({ape}) | ^ checkRd: (-1) ladderize.Rd:59: Lost braces; missing escapes or markup? 59 | \code{\link{rev.dendrogram}}, \code{\link{rotate}} ({dendextend}), \code{\link[ape]{rotate}} ({ape}) | ^ checkRd: (-1) prune.Rd:62: Lost braces; missing escapes or markup? 62 | \link{prune_leaf}, \link[ape]{drop.tip} {ape} | ^ checkRd: (-1) rllply.Rd:25: Lost braces; missing escapes or markup? 25 | following the naming convention in the {plyr} package | ^ checkRd: (-1) rotate.Rd:81: Lost braces; missing escapes or markup? 81 | The {ape} package has its own \code{\link[ape]{rotate}}({ape}) function | ^ checkRd: (-1) rotate.Rd:81: Lost braces; missing escapes or markup? 81 | The {ape} package has its own \code{\link[ape]{rotate}}({ape}) function | ^ checkRd: (-1) rotate.Rd:86: Lost braces; missing escapes or markup? 86 | Notice that if you will first load {ape} and only then {dendextend}, | ^ checkRd: (-1) rotate.Rd:86: Lost braces; missing escapes or markup? 86 | Notice that if you will first load {ape} and only then {dendextend}, | ^ checkRd: (-1) rotate.Rd:92: Lost braces; missing escapes or markup? 92 | The solution for this is that if you have {ape} installed on your machine, | ^ checkRd: (-1) rotate.Rd:93: Lost braces; missing escapes or markup? 93 | It will be loaded when you load {dendextend} (but after it). | ^ checkRd: (-1) rotate.Rd:134: Lost braces; missing escapes or markup? 134 | \code{\link{rev.dendrogram}}, \code{\link[ape]{rotate}} ({ape}), \link{ladderize} | ^ checkRd: (-1) unbranch.Rd:47: Lost braces; missing escapes or markup? 47 | \link[ape]{unroot} {ape} | ^ checkRd: (-1) untangle_DendSer.Rd:22: Lost braces 22 | This is a good (and fast) starting point for link{untangle_step_rotate_2side} | ^ * 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 ... 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 ... [12s/46s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [32s/57s] OK Running ‘test-all.R’ [32s/56s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [237s/513s] OK * checking PDF version of manual ... [17s/32s] OK * checking HTML version of manual ... [9s/21s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE