* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/hamlet.Rcheck’
* using R Under development (unstable) (2024-04-05 r86344)
* 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 ‘hamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hamlet’ version ‘0.9.6’
* 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 whether package ‘hamlet’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/hamlet-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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [11s/14s] OK
* checking Rd files ... NOTE
checkRd: (-1) hmap.Rd:87: Lost braces; missing escapes or markup?
    87 | The horizontal limits of the row hierarchical clustering. The horizontal limits of the heatmap are {a=leftlim[1], b=leftlim[2], c=xlim[1], d=xlim[2]} where the 'a' is where the row dendrogram begins, 'b' is where the row dendrogram ends, 'c' is where the heatmap itself begins, and 'd' is where the heatmap itself ends.
       |                                                                                                    ^
checkRd: (-1) hmap.Rd:91: Lost braces; missing escapes or markup?
    91 | The vertical limits of the row hierarchical clustering. The horizontal limits of the heatmap are {a=ylim[1], b=ylim[2], c=toplim[1], d=toplim[2]} where the 'a' is where the heatmap begins, 'b' is where the heatmap ends, 'c' is where the column dendrogram begins, and 'd' is where the column dendrogram ends.
       |                                                                                                  ^
checkRd: (-1) mix.binary.Rd:19: Lost braces; missing escapes or markup?
    19 | e.g. x = {red, green, blue, green} --> x_new = {{1,0,0}, {0,1,0}, {0,0,1}, {0,1,0}} where the dimensions in x_new are is_red, is_green and is_blue
       |          ^
checkRd: (-1) mix.binary.Rd:19: Lost braces
    19 | e.g. x = {red, green, blue, green} --> x_new = {{1,0,0}, {0,1,0}, {0,0,1}, {0,1,0}} where the dimensions in x_new are is_red, is_green and is_blue
       |                                                ^
checkRd: (-1) mix.binary.Rd:19: Lost braces; missing escapes or markup?
    19 | e.g. x = {red, green, blue, green} --> x_new = {{1,0,0}, {0,1,0}, {0,0,1}, {0,1,0}} where the dimensions in x_new are is_red, is_green and is_blue
       |                                                          ^
checkRd: (-1) mix.binary.Rd:19: Lost braces; missing escapes or markup?
    19 | e.g. x = {red, green, blue, green} --> x_new = {{1,0,0}, {0,1,0}, {0,0,1}, {0,1,0}} where the dimensions in x_new are is_red, is_green and is_blue
       |                                                                   ^
checkRd: (-1) mix.binary.Rd:19: Lost braces; missing escapes or markup?
    19 | e.g. x = {red, green, blue, green} --> x_new = {{1,0,0}, {0,1,0}, {0,0,1}, {0,1,0}} where the dimensions in x_new are is_red, is_green and is_blue
       |                                                                            ^
* 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 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 ... [20s/26s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [17s/23s] OK
* checking PDF version of manual ... [8s/14s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs