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This page was generated on 2025-09-25 12:06 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 873/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 3.99.0  (landing page)
Guangchuang Yu
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 2025)
git_url: https://git.bioconductor.org/packages/ggtree
git_branch: devel
git_last_commit: 58b3c7c
git_last_commit_date: 2025-09-17 02:33:48 -0400 (Wed, 17 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ggtree on kjohnson3

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: 3.99.0
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_3.99.0.tar.gz
StartedAt: 2025-09-24 19:41:13 -0400 (Wed, 24 Sep 2025)
EndedAt: 2025-09-24 19:41:49 -0400 (Wed, 24 Sep 2025)
EllapsedTime: 36.6 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_3.99.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ggtree.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggtree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggtree’ version ‘3.99.0’
* 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: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-3.22-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 ‘3.99.0’
** 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 (2025-09-10 r88807) -- "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 v3.99.0 Learn more at https://yulab-smu.top/contribution-tree-data/

Please cite:

Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan
Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. Ggtree: A serialized data
object for visualization of a phylogenetic tree and annotation data.
iMeta 2022, 1(4):e56. doi:10.1002/imt2.56
> 
> test_check("ggtree")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 14 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
  1.206   0.068   1.273 

Example timings

ggtree.Rcheck/ggtree-Ex.timings

nameusersystemelapsed
collapse0.2490.0080.258
expand0.1020.0010.103
facet-plot0.1120.0000.112
flip0.0950.0000.096
geom-hilight2.2920.0312.333
geom_balance0.1200.0000.121
geom_cladelab0.2030.0020.205
geom_label20.1220.0010.126
geom_point20.5940.0050.598
geom_rootedge0.3880.0020.390
geom_rootpoint0.2000.0010.201
geom_strip0.1360.0010.139
geom_striplab0.1200.0010.122
geom_tiplab0.1030.0010.103
geom_tiplab20.1120.0010.113
geom_tippoint0.0940.0000.095
geom_tree0.0640.0000.066
get_taxa_name0.0460.0000.047
ggdensitree1.1420.0051.148
ggexpand0.1300.0010.131
ggtree-format-painter0.1110.0010.113
ggtree0.1000.0010.101
label_pad0.0010.0000.001
open_tree0.1330.0010.134
reexports0.1540.0010.155
revts0.1290.0010.129
rotate0.1090.0000.109
rotate_tree0.1540.0010.157
scaleClade0.1140.0010.116
theme_tree0.1280.0010.137
theme_tree20.1490.0010.150
tree-layout0.6140.0060.626
viewClade0.1110.0010.111
xlim_expand0.1180.0010.118
xlim_tree0.1210.0000.121
zoomClade0.0000.0010.000