Guangchuang Yu
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ggtree |
| Branch: RELEASE_3_9 |
| Last Commit: 245e2ec |
| Last Changed Date: 2019-08-26 06:20:34 -0400 (Mon, 26 Aug 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:32:19 -0400 (Wed, 16 Oct 2019).
| Package 678/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ggtree 1.16.6 Guangchuang Yu
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ggtree |
| Version: 1.16.6 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggtree.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ggtree_1.16.6.tar.gz |
| StartedAt: 2019-10-16 04:03:49 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:05:36 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 107.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ggtree.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggtree.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ggtree_1.16.6.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ggtree.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '1.16.6' * 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 ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/geom_label2.Rd:52: file link 'geom_label' in package 'ggplot2' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:47: file link 'collapse' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:49: file link 'xlim' in package 'ggplot2' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:49: file link 'geom_label' in package 'ggplot2' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:51: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:55: file link 'read.beast' in package 'treeio' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:55: file link 'read.jtree' in package 'treeio' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:55: file link 'read.mrbayes' in package 'treeio' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ggtree.Rcheck/00install.out' for details. * 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 * 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 WARNING See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ggtree.Rcheck/00check.log' for details.
ggtree.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ggtree_1.16.6.tar.gz && rm -rf ggtree.buildbin-libdir && mkdir ggtree.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggtree.buildbin-libdir ggtree_1.16.6.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ggtree_1.16.6.zip && rm ggtree_1.16.6.tar.gz ggtree_1.16.6.zip
###
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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-TREEDATA html
add_TREEINFO html
add_colorbar html
annotation_image html
applyLayoutDaylight html
as.polytomy html
collapse html
decimal2Date html
dotFun html
expand html
facet_data html
facet_labeller html
facet_plot html
facet_widths html
flip html
geom_aline html
geom_balance html
geom_cladelabel html
geom_cladelabel2 html
geom_hilight html
geom_hilight_encircle html
geom_label2 html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/geom_label2.Rd:52: file link 'geom_label' in package 'ggplot2' does not exist and so has been treated as a topic
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
get.path html
getNodeAngle.df html
getNodesBreadthFirst.df html
getSubtree html
getSubtree.df html
getSubtreeUnrooted html
getSubtreeUnrooted.df html
getTreeArcAngles html
get_balance_position html
get_clade_position html
get_heatmap_column_position html
get_taxa_name html
ggtree-ggproto html
ggtree html
gheatmap html
gzoom-methods html
gzoom.phylo html
identify html
inset html
layoutDaylight html
layoutEqualAngle html
msaplot html
multiplot html
nodebar html
nodeid html
nodepie html
open_tree html
phylopic html
range_format html
reexports html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:47: file link 'collapse' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:49: file link 'xlim' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:49: file link 'geom_label' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:51: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:55: file link 'read.beast' in package 'treeio' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:55: file link 'read.jtree' in package 'treeio' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYdN19R/R.INSTALL16907a9d228/ggtree/man/reexports.Rd:55: file link 'read.mrbayes' in package 'treeio' does not exist and so has been treated as a topic
revts html
rotate html
rotateTreePoints.df html
rotate_tree html
scaleClade html
scale_color-methods html
scale_x_ggtree html
set_hilight_legend html
stat_balance html
stat_hilight html
subview html
theme_inset html
theme_tree html
theme_tree2 html
update-TREE html
viewClade html
xlim_expand html
xlim_tree 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_1.16.6.zip
* DONE (ggtree)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ggtree' successfully unpacked and MD5 sums checked
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ggtree.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 v1.16.6 For help: https://yulab-smu.github.io/treedata-book/
If you use ggtree in published research, please cite the most appropriate paper(s):
[36m-[39m 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
[36m-[39m 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: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
1.81 0.14 2.14
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ggtree.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 v1.16.6 For help: https://yulab-smu.github.io/treedata-book/
If you use ggtree in published research, please cite the most appropriate paper(s):
[36m-[39m 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
[36m-[39m 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: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
1.76 0.15 2.12
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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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