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) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).
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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 767/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ggtree 3.0.4 (landing page) Guangchuang Yu
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ggtree |
| Version: 3.0.4 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggtree.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ggtree_3.0.4.tar.gz |
| StartedAt: 2021-10-14 23:49:29 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:51:03 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 93.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ggtree.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggtree.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ggtree_3.0.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ggtree.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '3.0.4'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.13-bioc/meat/ggtree.Rcheck/00check.log'
for details.
ggtree.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ggtree_3.0.4.tar.gz && rm -rf ggtree.buildbin-libdir && mkdir ggtree.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggtree.buildbin-libdir ggtree_3.0.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ggtree_3.0.4.zip && rm ggtree_3.0.4.tar.gz ggtree_3.0.4.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 303k 100 303k 0 0 1137k 0 --:--:-- --:--:-- --:--:-- 1141k
install for i386
* 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: C:/Users/biocbuild/bbs-3.13-bioc/meat/ggtree.buildbin-libdir/00LOCK-ggtree/00new/ggtree/help/collapse.html
revts html
rotate html
rotateTreePoints html
rotate_tree html
scaleClade html
scale_color-methods html
scale_x_ggtree html
scale_x_range html
set_hilight_legend html
td_filter 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
install for x64
* installing *source* package 'ggtree' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggtree' as ggtree_3.0.4.zip
* DONE (ggtree)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ggtree' successfully unpacked and MD5 sums checked
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ggtree.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
2.60 0.17 2.92
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ggtree.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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 v3.0.4 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
2.43 0.03 2.45
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ggtree.Rcheck/examples_i386/ggtree-Ex.timings
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ggtree.Rcheck/examples_x64/ggtree-Ex.timings
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