Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-07-28 11:40 -0400 (Mon, 28 Jul 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 875/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggtree 3.16.3 (landing page) Guangchuang Yu
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
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: 2025-07-27 22:47:45 -0400 (Sun, 27 Jul 2025) |
EndedAt: 2025-07-27 22:48:52 -0400 (Sun, 27 Jul 2025) |
EllapsedTime: 67.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ggtree.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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.
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)
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: Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96 > > test_check("ggtree") [ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ] > > proc.time() user system elapsed 2.173 0.148 2.309
ggtree.Rcheck/ggtree-Ex.timings
name | user | system | elapsed | |
collapse | 0.285 | 0.004 | 0.288 | |
expand | 0.151 | 0.000 | 0.151 | |
facet-plot | 0.239 | 0.025 | 0.264 | |
flip | 0.172 | 0.003 | 0.174 | |
geom-hilight | 2.343 | 0.036 | 2.480 | |
geom_balance | 0.213 | 0.002 | 0.215 | |
geom_cladelab | 0.425 | 0.004 | 0.430 | |
geom_label2 | 0.203 | 0.002 | 0.203 | |
geom_point2 | 0.827 | 0.031 | 0.859 | |
geom_rootedge | 0.648 | 0.002 | 0.652 | |
geom_rootpoint | 0.252 | 0.000 | 0.252 | |
geom_strip | 0.154 | 0.000 | 0.154 | |
geom_striplab | 0.193 | 0.000 | 0.192 | |
geom_tiplab | 0.147 | 0.001 | 0.147 | |
geom_tiplab2 | 0.225 | 0.001 | 0.226 | |
geom_tippoint | 0.139 | 0.000 | 0.138 | |
geom_tree | 0.117 | 0.000 | 0.117 | |
get_taxa_name | 0.027 | 0.000 | 0.027 | |
ggdensitree | 1.450 | 0.028 | 1.479 | |
ggexpand | 0.197 | 0.002 | 0.199 | |
ggtree-format-painter | 0.178 | 0.001 | 0.178 | |
ggtree | 0.135 | 0.002 | 0.139 | |
label_pad | 0.001 | 0.000 | 0.001 | |
open_tree | 0.217 | 0.003 | 0.220 | |
reexports | 0.214 | 0.000 | 0.213 | |
revts | 0.139 | 0.000 | 0.138 | |
rotate | 0.146 | 0.000 | 0.146 | |
rotate_tree | 0.214 | 0.001 | 0.215 | |
scaleClade | 0.174 | 0.000 | 0.174 | |
theme_tree | 0.142 | 0.000 | 0.142 | |
theme_tree2 | 0.148 | 0.001 | 0.148 | |
tree-layout | 0.861 | 0.001 | 0.864 | |
viewClade | 0.193 | 0.000 | 0.194 | |
xlim_expand | 0.240 | 0.000 | 0.241 | |
xlim_tree | 0.241 | 0.000 | 0.242 | |
zoomClade | 0.000 | 0.000 | 0.001 | |