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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings ggtree_4.1.1.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ggtree.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ggtree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggtree’ version ‘4.1.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Guangchuang Yu <guangchuangyu@gmail.com>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.

The Title field should be in title case. Current version is:
  ‘an R package for visualization of tree and annotation data’
In title case that is:
  ‘An R Package for Visualization of Tree and Annotation Data’

The Description field should not start with the package name,
  'This package' or similar.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘add_TREEINFO.Rd’:
    https://doi.org/10.1093/molbev/msy194
  File ‘facet-plot.Rd’:
    https://doi.org/10.1093/molbev/msy194
  File ‘facet_data.Rd’:
    https://doi.org/10.1093/molbev/msy194
  File ‘geom_point2.Rd’:
    https://doi.org/10.1111/2041-210X.12628
    https://doi.org/10.1093/molbev/msy194
    https://doi.org/10.1002/cpbi.96
  File ‘geom_rootedge.Rd’:
    https://doi.org/10.1111/2041-210X.12628
  File ‘ggtree.Rd’:
    https://doi.org/10.1093/molbev/msy194
    https://doi.org/10.1111/2041-210X.12628
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ggtree’ can be installed ... OK
* checking installed package size ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
  ‘[ggfun:attacher]{%<+%}’ ‘[ggplot2:scale_manual]{scale_color_manual}’
  ‘[ggplot2:scale_manual]{scale_colour_manual}’
  ‘[ggplot2:scale_manual]{scale_fill_manual}’
  ‘[ggplot2:scale_continuous]{scale_x_continuous}’
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
geom-hilight 5.298  0.016   5.346
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ggtree.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL ggtree
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘ggtree’ ...
** this is package ‘ggtree’ version ‘4.1.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggtree)

R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ggtree)
ggtree v4.1.1 Learn more at https://yulab-smu.top/contribution-tree-data/

Please cite:

S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L
Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact
visualization of richly annotated phylogenetic data. Molecular Biology
and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166
> 
> test_check("ggtree")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 14 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
  2.286   0.171   2.445