Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:37:47 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 857/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggtree 3.10.1 (landing page) Guangchuang Yu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 3.10.1 |
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_3.10.1.tar.gz |
StartedAt: 2024-03-28 03:27:21 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 03:29:44 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 142.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ggtree.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_3.10.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/ggtree.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ggtree/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ggtree’ version ‘3.10.1’ * 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 R 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 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 ... OK * 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
ggtree.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ggtree ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘ggtree’ ... ** 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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (64-bit) 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 v3.10.1 For help: https://yulab-smu.top/treedata-book/ If you use the ggtree package suite in published research, please cite the appropriate paper(s): Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628 LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. doi: 10.1093/molbev/msz240 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 3 | SKIP 0 | PASS 14 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 14 ] > > proc.time() user system elapsed 4.409 0.409 4.838
ggtree.Rcheck/ggtree-Ex.timings
name | user | system | elapsed | |
attacher | 0.767 | 0.018 | 0.789 | |
collapse | 0.605 | 0.007 | 0.619 | |
expand | 0.315 | 0.029 | 0.349 | |
facet-plot | 0.427 | 0.023 | 0.451 | |
flip | 0.357 | 0.012 | 0.371 | |
geom-hilight | 3.560 | 0.026 | 3.607 | |
geom_balance | 0.462 | 0.005 | 0.471 | |
geom_cladelab | 0.844 | 0.010 | 0.857 | |
geom_label2 | 0.427 | 0.003 | 0.432 | |
geom_point2 | 1.800 | 0.017 | 1.828 | |
geom_rootedge | 1.399 | 0.009 | 1.416 | |
geom_rootpoint | 0.592 | 0.005 | 0.607 | |
geom_strip | 0.343 | 0.004 | 0.354 | |
geom_striplab | 0.433 | 0.003 | 0.454 | |
geom_tiplab | 0.316 | 0.003 | 0.323 | |
geom_tiplab2 | 0.501 | 0.003 | 0.524 | |
geom_tippoint | 0.301 | 0.003 | 0.314 | |
geom_tree | 0.271 | 0.003 | 0.288 | |
get_taxa_name | 0.054 | 0.001 | 0.055 | |
ggdensitree | 3.175 | 0.024 | 3.248 | |
ggexpand | 0.439 | 0.003 | 0.450 | |
ggtree-format-painter | 0.341 | 0.004 | 0.345 | |
ggtree | 0.273 | 0.003 | 0.278 | |
label_pad | 0.001 | 0.000 | 0.002 | |
open_tree | 0.423 | 0.003 | 0.426 | |
revts | 0.457 | 0.005 | 0.464 | |
rotate | 0.313 | 0.011 | 0.327 | |
rotate_tree | 0.431 | 0.003 | 0.435 | |
scaleClade | 0.349 | 0.003 | 0.353 | |
td_filter | 0.271 | 0.002 | 0.275 | |
theme_tree | 0.284 | 0.003 | 0.287 | |
theme_tree2 | 0.297 | 0.003 | 0.302 | |
tree-layout | 1.837 | 0.014 | 1.870 | |
viewClade | 0.421 | 0.003 | 0.574 | |
xlim_expand | 0.510 | 0.004 | 0.518 | |
xlim_tree | 0.507 | 0.003 | 0.514 | |
zoomClade | 0.000 | 0.001 | 0.001 | |