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This page was generated on 2024-05-04 11:37:51 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 867/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 3.12.0  (landing page)
Guangchuang Yu
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/ggtree
git_branch: RELEASE_3_19
git_last_commit: 87fbfbd
git_last_commit_date: 2024-04-30 10:41:21 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for ggtree on palomino3


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.

raw results


Summary

Package: ggtree
Version: 3.12.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggtree.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ggtree_3.12.0.tar.gz
StartedAt: 2024-05-04 03:57:11 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 03:58:47 -0400 (Sat, 04 May 2024)
EllapsedTime: 95.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ggtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggtree.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ggtree_3.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ggtree.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ggtree/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ggtree' version '3.12.0'
* 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 '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


Installation output

ggtree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ggtree
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 v3.12.0 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

G Yu. Data Integration, Manipulation and Visualization of Phylogenetic
Trees (1st ed.). Chapman and Hall/CRC. 2022. ISBN: 9781032233574

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 
   2.98    0.34    3.29 

Example timings

ggtree.Rcheck/ggtree-Ex.timings

nameusersystemelapsed
attacher0.460.010.47
collapse0.330.000.33
expand0.290.020.31
facet-plot0.240.050.29
flip0.180.000.17
geom-hilight1.930.011.96
geom_balance0.270.020.28
geom_cladelab0.50.00.5
geom_label20.300.010.31
geom_point20.970.020.99
geom_rootedge0.840.000.84
geom_rootpoint0.280.010.30
geom_strip0.190.000.18
geom_striplab0.310.000.32
geom_tiplab0.220.000.22
geom_tiplab20.270.000.26
geom_tippoint0.140.000.14
geom_tree0.140.000.14
get_taxa_name0.030.000.03
ggdensitree2.060.052.11
ggexpand0.200.000.21
ggtree-format-painter0.130.030.15
ggtree0.130.000.12
label_pad000
open_tree0.220.030.25
revts0.330.000.33
rotate0.140.000.14
rotate_tree0.260.000.27
scaleClade0.250.000.25
td_filter0.130.000.12
theme_tree0.170.000.17
theme_tree20.170.020.19
tree-layout0.970.051.02
viewClade0.190.000.18
xlim_expand0.340.010.36
xlim_tree0.390.000.39
zoomClade000