Back to Multiple platform build/check report for BioC 3.10
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for ggtree on malbec1

This page was generated on 2020-04-15 12:09:39 -0400 (Wed, 15 Apr 2020).

Package 704/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 2.0.4
Guangchuang Yu
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ggtree
Branch: RELEASE_3_10
Last Commit: e6958bd
Last Changed Date: 2020-04-13 05:29:47 -0400 (Mon, 13 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ggtree
Version: 2.0.4
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ggtree_2.0.4.tar.gz
StartedAt: 2020-04-15 02:46:17 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:47:31 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 74.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ggtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ggtree_2.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ggtree.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.0.4’
* 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-3.10-bioc/R/bin/R CMD INSTALL ggtree
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 v2.0.4  For help: https://yulab-smu.github.io/treedata-book/

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

- 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
- 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 12 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  2.860   0.076   3.113 

Example timings

ggtree.Rcheck/ggtree-Ex.timings

nameusersystemelapsed
add-TREEDATA0.4560.0080.485
dotFun0.0000.0000.001
facet-plot0.3200.0000.319
geom_tiplab0.2400.0040.245
ggdensitree1.1880.0321.224
ggtree0.1680.0000.166
theme_tree0.1840.0000.185
theme_tree20.2040.0040.208
update-TREE0.2120.0080.230