Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:27 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for tanggle on tokay2


To the developers/maintainers of the tanggle package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tanggle.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1928/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tanggle 1.0.0  (landing page)
Klaus Schliep
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/tanggle
git_branch: RELEASE_3_14
git_last_commit: b54fd2e
git_last_commit_date: 2021-10-26 13:12:10 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: tanggle
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tanggle.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings tanggle_1.0.0.tar.gz
StartedAt: 2022-04-13 03:53:03 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 03:54:51 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 107.4 seconds
RetCode: 0
Status:   OK  
CheckDir: tanggle.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tanggle.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings tanggle_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/tanggle.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'tanggle/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tanggle' version '1.0.0'
* 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 'tanggle' 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 ... NOTE
ggevonet: no visible global function definition for 'reorder'
minimize_overlap: no visible global function definition for 'reorder'
Undefined global functions or variables:
  reorder
Consider adding
  importFrom("stats", "reorder")
to your NAMESPACE file.
* 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 'tinytest.R'
 OK
** running tests for arch 'x64' ...
  Running 'tinytest.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-3.14-bioc/meat/tanggle.Rcheck/00check.log'
for details.

Installation output

tanggle.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/tanggle_1.0.0.tar.gz && rm -rf tanggle.buildbin-libdir && mkdir tanggle.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tanggle.buildbin-libdir tanggle_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL tanggle_1.0.0.zip && rm tanggle_1.0.0.tar.gz tanggle_1.0.0.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
 97  262k   97  255k    0     0   836k      0 --:--:-- --:--:-- --:--:--  838k
100  262k  100  262k    0     0   856k      0 --:--:-- --:--:-- --:--:--  856k

install for i386

* installing *source* package 'tanggle' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'tanggle'
    finding HTML links ... done
    geom_splitnet                           html  
    ggevonet                                html  
    ggsplitnet                              html  
    minimize_overlap                        html  
    node_depth_evonet                       html  
    tanggle-package                         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 'tanggle' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tanggle' as tanggle_1.0.0.zip
* DONE (tanggle)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'tanggle' successfully unpacked and MD5 sums checked

Tests output

tanggle.Rcheck/tests_i386/tinytest.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> if (require("tinytest", quietly=TRUE)){
+     test_package("tanggle")
+ }
Loading required package: ggplot2
Loading required package: ggtree
ggtree v3.2.1  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_tanggle.R................    0 tests    
Attaching package: 'ape'

The following object is masked from 'package:ggtree':

    rotate


test_tanggle.R................    0 tests    
test_tanggle.R................    0 tests    
test_tanggle.R................    1 tests OK 
test_tanggle.R................    1 tests OK 
test_tanggle.R................    2 tests OK 
test_tanggle.R................    2 tests OK 
test_tanggle.R................    2 tests OK 
test_tanggle.R................    3 tests OK 
test_tanggle.R................    3 tests OK 
test_tanggle.R................    3 tests OK 
test_tanggle.R................    3 tests OK 
test_tanggle.R................    3 tests OK 
test_tanggle.R................    4 tests OK 0.2s
All ok, 4 results (0.2s)
> 
> proc.time()
   user  system elapsed 
   2.81    0.26    3.06

tanggle.Rcheck/tests_x64/tinytest.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> if (require("tinytest", quietly=TRUE)){
+     test_package("tanggle")
+ }
Loading required package: ggplot2
Loading required package: ggtree
ggtree v3.2.1  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_tanggle.R................    0 tests    
Attaching package: 'ape'

The following object is masked from 'package:ggtree':

    rotate


test_tanggle.R................    0 tests    
test_tanggle.R................    0 tests    
test_tanggle.R................    1 tests OK 
test_tanggle.R................    1 tests OK 
test_tanggle.R................    2 tests OK 
test_tanggle.R................    2 tests OK 
test_tanggle.R................    2 tests OK 
test_tanggle.R................    3 tests OK 
test_tanggle.R................    3 tests OK 
test_tanggle.R................    3 tests OK 
test_tanggle.R................    3 tests OK 
test_tanggle.R................    3 tests OK 
test_tanggle.R................    4 tests OK 0.2s
All ok, 4 results (0.2s)
> 
> proc.time()
   user  system elapsed 
   3.43    0.17    3.59

Example timings

tanggle.Rcheck/examples_i386/tanggle-Ex.timings

nameusersystemelapsed
geom_splitnet0.330.020.38
ggevonet0.520.000.52
ggsplitnet0.170.000.17
minimize_overlap0.380.100.47
node_depth_evonet0.070.000.08

tanggle.Rcheck/examples_x64/tanggle-Ex.timings

nameusersystemelapsed
geom_splitnet0.290.030.38
ggevonet0.640.000.64
ggsplitnet0.200.040.25
minimize_overlap0.490.110.60
node_depth_evonet0.090.000.09