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This page was generated on 2025-07-24 11:41 -0400 (Thu, 24 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4563
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4601
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4542
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4578
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 875/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 3.16.3  (landing page)
Guangchuang Yu
Snapshot Date: 2025-07-21 13:40 -0400 (Mon, 21 Jul 2025)
git_url: https://git.bioconductor.org/packages/ggtree
git_branch: RELEASE_3_21
git_last_commit: 19798cf
git_last_commit_date: 2025-07-11 12:54:16 -0400 (Fri, 11 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for ggtree on nebbiolo1

To the developers/maintainers of the ggtree package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggtree.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ggtree
Version: 3.16.3
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ggtree_3.16.3.tar.gz
StartedAt: 2025-07-23 22:58:23 -0400 (Wed, 23 Jul 2025)
EndedAt: 2025-07-23 22:59:30 -0400 (Wed, 23 Jul 2025)
EllapsedTime: 67.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ggtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ggtree_3.16.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ggtree.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ggtree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggtree’ version ‘3.16.3’
* 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 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 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:element]{margin}’
  ‘[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 ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ggtree.Rcheck/00check.log’
for details.


Installation output

ggtree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ggtree
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ggtree’ ...
** this is package ‘ggtree’ version ‘3.16.3’
** 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)

Tests output

ggtree.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
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 v3.16.3 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 4 | SKIP 0 | PASS 14 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
  2.208   0.168   2.361 

Example timings

ggtree.Rcheck/ggtree-Ex.timings

nameusersystemelapsed
collapse0.2900.0090.300
expand0.1520.0000.152
facet-plot0.2550.0230.277
flip0.1720.0000.172
geom-hilight1.8940.0251.920
geom_balance0.2100.0050.214
geom_cladelab0.4100.0030.412
geom_label20.2080.0010.208
geom_point20.7760.0070.783
geom_rootedge0.6540.0300.684
geom_rootpoint0.4580.0010.459
geom_strip0.2320.0000.233
geom_striplab0.3840.0000.383
geom_tiplab0.2890.0020.291
geom_tiplab20.2470.0010.248
geom_tippoint0.1690.0010.175
geom_tree0.1570.0020.158
get_taxa_name0.0240.0020.025
ggdensitree1.4170.0321.448
ggexpand0.1990.0000.200
ggtree-format-painter0.1780.0020.182
ggtree0.1280.0000.128
label_pad0.0010.0000.001
open_tree0.2080.0000.209
reexports0.210.000.21
revts0.1390.0000.139
rotate0.1440.0000.143
rotate_tree0.2060.0000.207
scaleClade0.1700.0010.170
theme_tree0.1440.0010.146
theme_tree20.1460.0010.147
tree-layout0.8740.0020.877
viewClade0.2000.0000.199
xlim_expand0.2470.0000.250
xlim_tree0.2440.0000.245
zoomClade000