Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:07:26 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 biodbKegg on machv2


To the developers/maintainers of the biodbKegg package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbKegg.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 178/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbKegg 1.0.0  (landing page)
Pierrick Roger
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/biodbKegg
git_branch: RELEASE_3_14
git_last_commit: 5bb8a8a
git_last_commit_date: 2021-10-26 13:13:42 -0500 (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: biodbKegg
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbKegg_1.0.0.tar.gz
StartedAt: 2022-01-20 10:35:19 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 10:52:46 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 1046.9 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbKegg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbKegg_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/biodbKegg.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbKegg/DESCRIPTION’ ... OK
* this is package ‘biodbKegg’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biodbKegg’ can be installed ... OK
* checking installed package size ... OK
* checking package 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
KeggEnzymeConn   7.159  0.262   8.668
KeggCompoundConn 4.894  0.614   6.364
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

biodbKegg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbKegg
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘biodbKegg’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (biodbKegg)

Tests output

biodbKegg.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbKegg)
> Sys.setenv(TESTTHAT_REPORTER = "summary")
> test_check("biodbKegg")
trying URL 'https://www.kegg.jp/kegg/pathway/map/map00260.png'
downloaded 44 KB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1593 ]
> 
> proc.time()
   user  system elapsed 
224.626  13.285 945.558 

Example timings

biodbKegg.Rcheck/biodbKegg-Ex.timings

nameusersystemelapsed
KeggCircle0.0140.0010.016
KeggCompoundConn4.8940.6146.364
KeggCompoundEntry0.7000.0100.713
KeggConn0.4890.0080.499
KeggEntry0.6330.0100.644
KeggEnzymeConn7.1590.2628.668
KeggEnzymeEntry0.6650.0140.680
KeggGenesConn0.7710.0110.785
KeggGenesEntry0.7360.0110.749
KeggGlycanConn0.5700.0110.584
KeggGlycanEntry0.7350.0120.748
KeggModuleConn0.6870.0110.701
KeggModuleEntry0.6090.0120.622
KeggOrthologyConn0.7860.0100.800
KeggOrthologyEntry0.8440.0160.936
KeggPathwayConn3.0270.0273.069
KeggPathwayEntry0.6590.0110.672
KeggReactionConn0.6260.0100.638
KeggReactionEntry0.6410.0110.653
KeggRect0.0060.0010.006
KeggShape0.0010.0010.002