Guangchuang Yu
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/ggtree |
| git_branch: master |
| git_last_commit: b448e58 |
| git_last_commit_date: 2021-12-10 04:53:25 -0400 (Fri, 10 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:39 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 783/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ggtree 3.3.1 (landing page) Guangchuang Yu
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ggtree |
| Version: 3.3.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggtree.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ggtree_3.3.1.tar.gz |
| StartedAt: 2022-03-17 19:12:42 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:13:46 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 64.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ggtree.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggtree.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ggtree_3.3.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ggtree.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggtree/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ggtree' version '3.3.1'
* 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 ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
examples 3.7Mb
* 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: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/ggtree.Rcheck/00check.log'
for details.
ggtree.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ggtree
###
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##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ggtree' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ggtree'
finding HTML links ... done
Date2decimal html
add_TREEINFO html
add_colorbar html
applyLayoutDaylight html
as.polytomy html
attacher html
collapse html
decimal2Date html
expand html
facet-plot html
facet_data html
facet_labeller html
facet_widths html
flip html
geom-hilight html
geom_aline html
geom_balance html
geom_cladelab html
geom_cladelabel html
geom_cladelabel2 html
geom_label2 html
geom_motif html
geom_nodelab html
geom_nodelab2 html
geom_nodepoint html
geom_point2 html
geom_range html
geom_rootedge html
geom_rootpoint html
geom_segment2 html
geom_strip html
geom_taxalink html
geom_text2 html
geom_tiplab html
geom_tiplab2 html
geom_tippoint html
geom_tree html
geom_tree2 html
geom_treescale html
geom_zoom_clade html
get.path html
getNodeAngle.df html
getNodesBreadthFirst.df html
getSubtree html
getSubtree.df html
getSubtreeUnrooted html
getSubtreeUnrooted.df html
getTreeArcAngles html
get_clade_position html
get_heatmap_column_position html
get_taxa_name html
ggdensitree html
ggexpand html
ggtree-format-painter html
ggtree-ggproto html
ggtree html
gheatmap html
gzoom-methods html
gzoom.phylo html
identify html
inset html
label_pad html
layoutDaylight html
layoutEqualAngle html
msaplot html
multiplot html
nodebar html
nodepie html
open_tree html
range_format html
reexports html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-ggtree/00new/ggtree/help/collapse.html
revts html
rotate html
rotateTreePoints html
rotate_tree html
scale-color-subtree html
scaleClade html
scale_color-methods html
scale_x_ggtree html
scale_x_range html
set_hilight_legend html
td_filter html
td_mutate html
td_unnest html
theme_dendrogram html
theme_inset html
theme_tree html
theme_tree2 html
tree-layout html
viewClade html
xlim_expand html
xlim_tree html
zoomClade html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'SRAdb' is missing or broken
done
ggtree.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.
> library(testthat)
> library(ggtree)
ggtree v3.3.1 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 14 ]
>
> proc.time()
user system elapsed
1.92 0.18 2.10
ggtree.Rcheck/ggtree-Ex.timings
| name | user | system | elapsed | |
| attacher | 0.36 | 0.02 | 0.37 | |
| facet-plot | 0.19 | 0.03 | 0.22 | |
| geom-hilight | 1.23 | 0.00 | 1.23 | |
| geom_cladelab | 0.42 | 0.00 | 0.42 | |
| geom_point2 | 0.88 | 0.00 | 0.88 | |
| geom_rootedge | 0.56 | 0.00 | 0.56 | |
| geom_rootpoint | 0.23 | 0.00 | 0.23 | |
| geom_tiplab | 0.14 | 0.00 | 0.14 | |
| get_taxa_name | 0.03 | 0.00 | 0.04 | |
| ggdensitree | 1.85 | 0.00 | 1.84 | |
| ggtree-format-painter | 0.15 | 0.00 | 0.16 | |
| ggtree | 0.13 | 0.00 | 0.12 | |
| label_pad | 0 | 0 | 0 | |
| td_filter | 0.08 | 0.00 | 0.08 | |
| theme_tree | 0.12 | 0.01 | 0.14 | |
| theme_tree2 | 0.16 | 0.00 | 0.16 | |