Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-03 11:38:24 -0400 (Fri, 03 May 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" | 4660 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
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 838/2230 | 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 | 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: 3.13.0 |
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: 2024-05-02 05:06:11 -0400 (Thu, 02 May 2024) |
EndedAt: 2024-05-02 05:09:16 -0400 (Thu, 02 May 2024) |
EllapsedTime: 184.7 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed geom-hilight 4.182 0.048 5.183 * 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 Guangchuang Yu. Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st edition). Chapman and Hall/CRC. 2022, doi:10.1201/9781003279242 G Yu. Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st ed.). Chapman and Hall/CRC. 2022. ISBN: 9781032233574 > > test_check("ggtree") [ FAIL 0 | WARN 3 | SKIP 0 | PASS 14 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 14 ] > > proc.time() user system elapsed 4.878 0.428 6.119
ggtree.Rcheck/ggtree-Ex.timings
name | user | system | elapsed | |
attacher | 0.888 | 0.026 | 1.096 | |
collapse | 0.548 | 0.007 | 0.698 | |
expand | 0.372 | 0.004 | 0.455 | |
facet-plot | 0.630 | 0.041 | 0.820 | |
flip | 0.411 | 0.012 | 0.501 | |
geom-hilight | 4.182 | 0.048 | 5.183 | |
geom_balance | 0.537 | 0.007 | 0.660 | |
geom_cladelab | 0.980 | 0.011 | 1.226 | |
geom_label2 | 0.511 | 0.010 | 0.675 | |
geom_point2 | 2.088 | 0.024 | 2.492 | |
geom_rootedge | 1.608 | 0.014 | 1.867 | |
geom_rootpoint | 0.682 | 0.006 | 0.791 | |
geom_strip | 0.389 | 0.006 | 0.450 | |
geom_striplab | 0.506 | 0.008 | 0.590 | |
geom_tiplab | 0.357 | 0.004 | 0.421 | |
geom_tiplab2 | 0.584 | 0.005 | 0.688 | |
geom_tippoint | 0.325 | 0.004 | 0.388 | |
geom_tree | 0.309 | 0.004 | 0.371 | |
get_taxa_name | 0.060 | 0.001 | 0.066 | |
ggdensitree | 3.577 | 0.032 | 4.233 | |
ggexpand | 0.523 | 0.006 | 0.628 | |
ggtree-format-painter | 0.392 | 0.005 | 0.460 | |
ggtree | 0.308 | 0.004 | 0.368 | |
label_pad | 0.001 | 0.000 | 0.002 | |
open_tree | 0.682 | 0.011 | 0.819 | |
revts | 0.338 | 0.005 | 0.384 | |
rotate | 0.346 | 0.004 | 0.381 | |
rotate_tree | 0.509 | 0.004 | 0.596 | |
scaleClade | 0.416 | 0.003 | 0.483 | |
td_filter | 0.323 | 0.004 | 0.378 | |
theme_tree | 0.336 | 0.005 | 0.395 | |
theme_tree2 | 0.352 | 0.004 | 0.406 | |
tree-layout | 2.123 | 0.022 | 2.481 | |
viewClade | 0.482 | 0.004 | 0.541 | |
xlim_expand | 0.593 | 0.006 | 0.692 | |
xlim_tree | 0.600 | 0.006 | 0.695 | |
zoomClade | 0.000 | 0.001 | 0.001 | |