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This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).

CHECK results for ggtreeExtra on tokay2

To the developers/maintainers of the ggtreeExtra package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggtreeExtra.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.

raw results

Package 768/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtreeExtra 1.2.3  (landing page)
Shuangbin Xu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/ggtreeExtra
git_branch: RELEASE_3_13
git_last_commit: 759f5d0
git_last_commit_date: 2021-09-09 22:58:29 -0400 (Thu, 09 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ggtreeExtra
Version: 1.2.3
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggtreeExtra.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ggtreeExtra_1.2.3.tar.gz
StartedAt: 2021-10-14 23:49:58 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:51:15 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 77.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ggtreeExtra.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggtreeExtra.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ggtreeExtra_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ggtreeExtra.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 'ggtreeExtra/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ggtreeExtra' version '1.2.3'
* 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 'ggtreeExtra' 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 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: OK


Installation output

ggtreeExtra.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ggtreeExtra_1.2.3.tar.gz && rm -rf ggtreeExtra.buildbin-libdir && mkdir ggtreeExtra.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggtreeExtra.buildbin-libdir ggtreeExtra_1.2.3.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ggtreeExtra_1.2.3.zip && rm ggtreeExtra_1.2.3.tar.gz ggtreeExtra_1.2.3.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
 22  442k   22   98k    0     0   518k      0 --:--:-- --:--:-- --:--:--  517k
100  442k  100  442k    0     0  1453k      0 --:--:-- --:--:-- --:--:-- 1454k

install for i386

* installing *source* package 'ggtreeExtra' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ggtreeExtra'
    finding HTML links ... done
    PositionJitterdodgex                    html  
    PositionJitterx                         html  
    geom_fruit                              html  
    geom_fruit_list                         html  
    ggplot2-ggproto                         html  
    position_dodgex                         html  
    position_identityx                      html  
    position_jitterdodgex                   html  
    position_jitterx                        html  
    position_points_jitterx                 html  
    finding level-2 HTML links ... done

    position_points_sinax                   html  
    position_raincloudx                     html  
    position_stackx                         html  
    reexports                               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 'ggtreeExtra' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggtreeExtra' as ggtreeExtra_1.2.3.zip
* DONE (ggtreeExtra)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ggtreeExtra' successfully unpacked and MD5 sums checked

Tests output

ggtreeExtra.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(ggtreeExtra)
ggtreeExtra v1.2.3  For help: https://yulab-smu.top/treedata-book/

If you use ggtreeExtra in published research, please cite the paper:

S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166


> 
> test_check("ggtreeExtra")
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


[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   1.90    0.14    2.01 

ggtreeExtra.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(ggtreeExtra)
ggtreeExtra v1.2.3  For help: https://yulab-smu.top/treedata-book/

If you use ggtreeExtra in published research, please cite the paper:

S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166


> 
> test_check("ggtreeExtra")
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


[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   1.82    0.20    2.01 

Example timings

ggtreeExtra.Rcheck/examples_i386/ggtreeExtra-Ex.timings

nameusersystemelapsed
geom_fruit0.180.040.20
geom_fruit_list1.950.021.97
position_dodgex1.030.001.03
position_identityx0.250.000.25
position_jitterx0.610.000.61
position_stackx0.250.000.25

ggtreeExtra.Rcheck/examples_x64/ggtreeExtra-Ex.timings

nameusersystemelapsed
geom_fruit0.190.020.21
geom_fruit_list2.140.012.16
position_dodgex1.10.01.1
position_identityx0.280.000.28
position_jitterx0.670.000.67
position_stackx0.280.000.28