* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dartR.Rcheck’
* using R Under development (unstable) (2024-04-29 r86495)
* 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 ‘dartR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dartR’ version ‘2.9.7’
* 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 ‘dartR’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/dartR-00install.html' 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [20s/25s] OK
* checking whether the package can be loaded with stated dependencies ... [20s/24s] OK
* checking whether the package can be unloaded cleanly ... [20s/26s] OK
* checking whether the namespace can be loaded with stated dependencies ... [19s/23s] OK
* checking whether the namespace can be unloaded cleanly ... [20s/25s] OK
* checking loading without being on the library search path ... [20s/22s] OK
* checking whether startup messages can be suppressed ... [20s/21s] 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 ... [193s/234s] OK
* checking Rd files ... [3s/4s] NOTE
checkRd: (-1) gl.filter.maf.Rd:7: Lost braces; missing escapes or markup?
     7 |  {adegenet} object}
       |  ^
checkRd: (-1) gl.pcoa.Rd:68: Lost braces; missing escapes or markup?
    68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}
       |                                                 ^
checkRd: (-1) gl.play.history.Rd:17: Lost braces
    17 | code{x2@other$history[c(1,4,5)]}). [optional].}
       |     ^
checkRd: (-1) utils.jackknife.Rd:49: Lost braces
    49 | bold{Note} that when n is very small, jackknife resampling is not recommended.
       |     ^
checkRd: (-1) utils.jackknife.Rd:51: Lost braces
    51 | Parallel computation is implemented. The argument code{n.cores} indicates the 
       |                                                       ^
* 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 ... [5s/6s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [137s/166s] OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
gl.plot.heatmap 5.835  0.001   7.227
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [21s/26s] OK
  Running ‘testthat.R’ [21s/26s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [4s/5s] OK
* checking PDF version of manual ... [19s/23s] OK
* checking HTML version of manual ... [12s/20s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE