Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 842/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggtree 3.13.0 (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 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 3.13.0 |
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_3.13.0.tar.gz |
StartedAt: 2024-06-10 04:16:56 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 04:19:52 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 176.1 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_3.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ggtree.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ggtree/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ggtree’ version ‘3.13.0’ * 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 ... 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 ... 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/4.4-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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 v3.13.0 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 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 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 3 | SKIP 0 | PASS 14 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 14 ] > > proc.time() user system elapsed 4.848 0.430 5.909
ggtree.Rcheck/ggtree-Ex.timings
name | user | system | elapsed | |
attacher | 0.869 | 0.025 | 0.917 | |
collapse | 0.539 | 0.004 | 0.552 | |
expand | 0.514 | 0.004 | 0.528 | |
facet-plot | 0.485 | 0.039 | 0.533 | |
flip | 0.389 | 0.009 | 0.400 | |
geom-hilight | 4.107 | 0.035 | 4.383 | |
geom_balance | 0.527 | 0.005 | 0.580 | |
geom_cladelab | 0.988 | 0.010 | 1.083 | |
geom_label2 | 0.518 | 0.005 | 0.546 | |
geom_point2 | 2.070 | 0.029 | 2.365 | |
geom_rootedge | 1.569 | 0.015 | 1.827 | |
geom_rootpoint | 0.663 | 0.005 | 0.780 | |
geom_strip | 0.383 | 0.004 | 0.459 | |
geom_striplab | 0.489 | 0.005 | 0.571 | |
geom_tiplab | 0.357 | 0.006 | 0.411 | |
geom_tiplab2 | 0.575 | 0.005 | 0.629 | |
geom_tippoint | 0.327 | 0.003 | 0.372 | |
geom_tree | 0.302 | 0.003 | 0.340 | |
get_taxa_name | 0.060 | 0.002 | 0.072 | |
ggdensitree | 3.532 | 0.032 | 4.196 | |
ggexpand | 0.514 | 0.008 | 0.632 | |
ggtree-format-painter | 0.391 | 0.007 | 0.467 | |
ggtree | 0.301 | 0.004 | 0.333 | |
label_pad | 0.001 | 0.001 | 0.002 | |
open_tree | 0.661 | 0.010 | 0.762 | |
revts | 0.336 | 0.007 | 0.388 | |
rotate | 0.342 | 0.005 | 0.421 | |
rotate_tree | 0.504 | 0.004 | 0.613 | |
scaleClade | 0.402 | 0.005 | 0.483 | |
td_filter | 0.317 | 0.004 | 0.372 | |
theme_tree | 0.342 | 0.006 | 0.423 | |
theme_tree2 | 0.345 | 0.006 | 0.398 | |
tree-layout | 2.138 | 0.030 | 2.697 | |
viewClade | 0.476 | 0.006 | 0.561 | |
xlim_expand | 0.586 | 0.009 | 0.732 | |
xlim_tree | 0.592 | 0.012 | 0.711 | |
zoomClade | 0.000 | 0.001 | 0.001 | |