Back to Multiple platform build/check report for BioC 3.13
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).

CHECK results for ggtree on nebbiolo1

To the developers/maintainers of the ggtree package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 767/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 3.0.4  (landing page)
Guangchuang Yu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/ggtree
git_branch: RELEASE_3_13
git_last_commit: 7a83be2
git_last_commit_date: 2021-08-20 03:07:31 -0400 (Fri, 20 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ggtree
Version: 3.0.4
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ggtree_3.0.4.tar.gz
StartedAt: 2021-10-14 10:00:57 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:01:46 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 49.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ggtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ggtree_3.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ggtree.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggtree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggtree’ version ‘3.0.4’
* 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 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


Installation output

ggtree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ggtree
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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)

Tests output

ggtree.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 v3.0.4  For help: https://yulab-smu.top/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
3. 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


> 
> test_check("ggtree")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
  1.805   0.095   1.882 

Example timings

ggtree.Rcheck/ggtree-Ex.timings

nameusersystemelapsed
attacher0.2680.0080.276
facet-plot0.1630.0000.163
geom-hilight0.250.000.25
geom_cladelab0.4300.0040.434
geom_point20.7670.0000.768
geom_rootedge0.5590.0200.578
geom_rootpoint0.1820.0000.182
geom_tiplab0.1040.0000.104
get_taxa_name0.0220.0000.022
ggdensitree1.2050.0041.209
ggtree-format-painter0.1140.0040.118
ggtree0.0850.0020.089
label_pad0.0000.0000.001
td_filter0.0860.0040.090
theme_tree0.0990.0000.099
theme_tree20.1070.0000.107