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This page was generated on 2025-08-30 12:04 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 868/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 3.17.1  (landing page)
Guangchuang Yu
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025)
git_url: https://git.bioconductor.org/packages/ggtree
git_branch: devel
git_last_commit: 1444d4d
git_last_commit_date: 2025-07-11 12:45:38 -0400 (Fri, 11 Jul 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 nebbiolo2

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: 3.17.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ggtree_3.17.1.tar.gz
StartedAt: 2025-08-29 23:12:19 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 23:13:27 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 68.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ggtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ggtree_3.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ggtree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggtree’ version ‘3.17.1’
* 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-3.22-bioc/meat/ggtree.Rcheck/00check.log’
for details.


Installation output

ggtree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ggtree
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ggtree’ ...
** this is package ‘ggtree’ version ‘3.17.1’
** 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)

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 v3.17.1 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 4 | SKIP 0 | PASS 14 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
  2.258   0.122   2.367 

Example timings

ggtree.Rcheck/ggtree-Ex.timings

nameusersystemelapsed
collapse0.3310.0100.341
expand0.1680.0830.250
facet-plot0.4750.0150.490
flip0.3470.0010.347
geom-hilight2.3110.0352.365
geom_balance0.2220.0000.221
geom_cladelab0.4570.0040.461
geom_label20.2100.0250.236
geom_point20.8040.0110.815
geom_rootedge0.6880.0030.690
geom_rootpoint0.2810.0000.281
geom_strip0.1570.0000.158
geom_striplab0.1950.0010.195
geom_tiplab0.1480.0000.148
geom_tiplab20.2240.0000.224
geom_tippoint0.1360.0000.137
geom_tree0.1210.0000.121
get_taxa_name0.0260.0000.027
ggdensitree1.4770.0321.509
ggexpand0.2420.0000.242
ggtree-format-painter0.1720.0020.175
ggtree0.1290.0010.129
label_pad0.0000.0000.001
open_tree0.2100.0020.213
reexports0.2190.0000.219
revts0.1440.0010.145
rotate0.1510.0000.150
rotate_tree0.2040.0010.205
scaleClade0.1860.0010.186
theme_tree0.1380.0000.138
theme_tree20.1420.0000.142
tree-layout0.9370.0010.938
viewClade0.2050.0000.205
xlim_expand0.2480.0000.247
xlim_tree0.2630.0010.264
zoomClade000