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This page was generated on 2025-07-24 11:47 -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 kjohnson1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggtree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggtree_3.16.3.tar.gz
StartedAt: 2025-07-22 21:40:09 -0400 (Tue, 22 Jul 2025)
EndedAt: 2025-07-22 21:41:28 -0400 (Tue, 22 Jul 2025)
EllapsedTime: 79.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ggtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggtree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggtree_3.16.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ggtree.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ggtree.Rcheck/00check.log’
for details.


Installation output

ggtree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ggtree
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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:

Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods
for mapping and visualizing associated data on phylogeny using ggtree.
Molecular Biology and Evolution. 2018, 35(12):3041-3043.
doi:10.1093/molbev/msy194
> 
> test_check("ggtree")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
  2.651   0.203   2.843 

Example timings

ggtree.Rcheck/ggtree-Ex.timings

nameusersystemelapsed
collapse0.3350.0080.343
expand0.2210.0020.223
facet-plot0.1980.0030.201
flip0.1860.0030.189
geom-hilight1.9250.0301.956
geom_balance0.2320.0030.238
geom_cladelab0.4230.0060.430
geom_label20.2040.0020.207
geom_point20.9180.0130.937
geom_rootedge0.6480.0060.655
geom_rootpoint0.2780.0040.281
geom_strip0.1640.0020.166
geom_striplab0.4130.0080.422
geom_tiplab0.1640.0070.171
geom_tiplab20.2170.0020.219
geom_tippoint0.1360.0010.137
geom_tree0.1250.0020.143
get_taxa_name0.0400.0010.052
ggdensitree0.8640.0160.923
ggexpand0.1250.0020.129
ggtree-format-painter0.0990.0030.104
ggtree0.1180.0020.120
label_pad0.0010.0000.001
open_tree0.2110.0020.213
reexports0.2060.0030.208
revts0.1420.0010.143
rotate0.1400.0010.142
rotate_tree0.2560.0030.259
scaleClade0.1940.0030.196
theme_tree0.1680.0020.170
theme_tree20.1640.0020.166
tree-layout0.9320.0110.943
viewClade0.2100.0020.212
xlim_expand0.2690.0020.272
xlim_tree0.2470.0020.250
zoomClade000