* using log directory ‘/srv/hornik/tmp/CRAN_pretest/mycolorsTB.Rcheck’
* using R Under development (unstable) (2025-07-06 r88390)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux 13 (trixie)
* using session charset: UTF-8
* checking for file ‘mycolorsTB/DESCRIPTION’ ... OK
* this is package ‘mycolorsTB’ version ‘0.1.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/5s] NOTE
Maintainer: ‘Paula Ruiz-Rodriguez <paula.ruiz.rodriguez@csic.es>’

New submission

Possibly misspelled words in DESCRIPTION:
  Mycobacterium (2:28, 7:74)
* 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 ‘mycolorsTB’ can be installed ... [1s/1s] OK
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘ape’ ‘ggtree’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] NOTE
plot_tb_cladogram: no visible binding for global variable ‘label’
plot_tb_tree: no visible binding for global variable ‘label’
view_palette: no visible binding for global variable ‘name’
view_palette: no visible binding for global variable ‘hex’
Undefined global functions or variables:
  hex label name
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘classicTB’ ‘mycolors’ ‘pathogenomics’ ‘plot_tb_cladogram’
  ‘plot_tb_tree’ ‘scale_color_classicTB’ ‘scale_color_mycolors’
  ‘scale_fill_classicTB’ ‘scale_fill_mycolors’ ‘tb_palette’
  ‘view_palette’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in Rd file 'hello.Rd' but not in code:
  ‘hello’

* 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 ... [0s/0s] ERROR
Running examples in ‘mycolorsTB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hello
> ### Title: Hello, World!
> ### Aliases: hello
> 
> ### ** Examples
> 
> hello()
Error in hello() : could not find function "hello"
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2s/2s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘use-mycolors.Rmd’ using rmarkdown

Quitting from use-mycolors.Rmd:77-80 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'ape'
---
Backtrace:
    ▆
 1. ├─mycolorsTB::plot_tb_tree(tree_text)
 2. └─base::loadNamespace(x)
 3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 4.     └─base (local) withOneRestart(expr, restarts[[1L]])
 5.       └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'use-mycolors.Rmd' failed with diagnostics:
there is no package called 'ape'
--- failed re-building ‘use-mycolors.Rmd’

SUMMARY: processing the following file failed:
  ‘use-mycolors.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 3 WARNINGs, 2 NOTEs