Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:05:35 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for ggtreeDendro on palomino4


To the developers/maintainers of the ggtreeDendro package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggtreeDendro.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 817/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtreeDendro 1.0.0  (landing page)
Guangchuang Yu
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/ggtreeDendro
git_branch: RELEASE_3_16
git_last_commit: 645a8eb
git_last_commit_date: 2022-11-01 11:27:41 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ggtreeDendro
Version: 1.0.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggtreeDendro.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ggtreeDendro_1.0.0.tar.gz
StartedAt: 2023-04-11 01:59:38 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 02:00:29 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 51.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ggtreeDendro.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggtreeDendro.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ggtreeDendro_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/ggtreeDendro.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ggtreeDendro/DESCRIPTION' ... OK
* this is package 'ggtreeDendro' version '1.0.0'
* 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 whether package 'ggtreeDendro' 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

ggtreeDendro.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL ggtreeDendro
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'ggtreeDendro' ...
** 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 (ggtreeDendro)

Tests output

ggtreeDendro.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(ggtreeDendro)
Loading required package: ggtree
ggtree v3.6.2 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, 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

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
Registered S3 method overwritten by 'ggtreeDendro':
  method                   from  
  ggplot_add.color_subtree ggtree

Attaching package: 'ggtreeDendro'

The following objects are masked from 'package:ggtree':

    scale_color_subtree, scale_colour_subtree

> 
> test_check("ggtreeDendro")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   1.71    0.28    1.93 

Example timings

ggtreeDendro.Rcheck/ggtreeDendro-Ex.timings

nameusersystemelapsed
autoplot0.380.030.43
geom-line-cutree0.290.020.31
scale-color-subtree0.340.000.35