* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/spiralize.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* 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 ‘spiralize/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spiralize’ version ‘1.0.6’
* 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 ‘spiralize’ can be installed ... [15s/21s] OK
* 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 ... [27s/33s] OK
* checking Rd files ... NOTE
checkRd: (-1) cartesian_to_xy.Rd:21: Lost braces; missing escapes or markup?
    21 | in the polar coordinate system, r_k and r_{k+1} are the radius of the two loops at theta + 2*pi*a and theta + 2*pi*(a+1) that below and above the data point,
       |                                           ^
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘spiralize-Ex.R’ failed
The error most likely occurred in:

> ### Name: phylo_to_dendrogram
> ### Title: Convert a phylo object to a dendrogram object
> ### Aliases: phylo_to_dendrogram
> 
> ### ** Examples
> 
> require(ape)
Loading required package: ape
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ape’
> data(bird.families)
Warning in data(bird.families) : data set ‘bird.families’ not found
> d = phylo_to_dendrogram(bird.families)
Error: object 'bird.families' not found
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [12s/17s] 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: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/spiralize.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:30.88, 100.75 + 12.49