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CHECK report for ggtree on tokay2

This page was generated on 2019-10-16 12:32:19 -0400 (Wed, 16 Oct 2019).

Package 678/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 1.16.6
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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###
### 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.



Installation output

ggtree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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  264k  100  264k    0     0  2671k      0 --:--:-- --:--:-- --:--:-- 2848k

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

Tests output

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):

- 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
- 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 

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):

- 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
- 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 

Example timings

ggtree.Rcheck/examples_i386/ggtree-Ex.timings

nameusersystemelapsed
add-TREEDATA0.230.000.31
dotFun000
facet_plot0.250.020.27
geom_tiplab0.250.000.25
ggtree0.170.010.18
gzoom.phylo0.630.020.72
theme_tree0.160.000.16
theme_tree20.130.000.13
update-TREE0.150.000.15

ggtree.Rcheck/examples_x64/ggtree-Ex.timings

nameusersystemelapsed
add-TREEDATA0.250.000.25
dotFun000
facet_plot0.260.020.28
geom_tiplab0.220.000.22
ggtree0.170.000.17
gzoom.phylo0.520.000.52
theme_tree0.170.000.17
theme_tree20.140.020.16
update-TREE0.160.010.17