Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:06 -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 BiocPkgTools on nebbiolo2


To the developers/maintainers of the BiocPkgTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/BiocPkgTools.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 166/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.12.2  (landing page)
Sean Davis
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/BiocPkgTools
git_branch: RELEASE_3_14
git_last_commit: 19280c6
git_last_commit_date: 2021-11-04 13:57:14 -0400 (Thu, 04 Nov 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: BiocPkgTools
Version: 1.12.2
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BiocPkgTools_1.12.2.tar.gz
StartedAt: 2022-04-12 06:33:30 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:35:54 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 143.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BiocPkgTools_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BiocPkgTools.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocPkgTools’ version ‘1.12.2’
* 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 ‘BiocPkgTools’ 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
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocManager:::.repositories’ ‘BiocManager:::.repositories_bioc’
  ‘BiocManager:::.version_bioc’
  See the note in ?`:::` about the use of this operator.
* 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
biocBuildReport       5.148  2.885   6.910
pkgCombDependencyGain 4.635  0.108   5.660
pkgDepMetrics         4.315  0.109   5.297
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.



Installation output

BiocPkgTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL BiocPkgTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘BiocPkgTools’ ...
** 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 (BiocPkgTools)

Tests output

BiocPkgTools.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(BiocPkgTools)
Loading required package: htmlwidgets
> 
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.org/checkResults/3.14/bioc-LATEST/report.tgz'
Content type 'application/x-gzip' length 61279682 bytes (58.4 MB)
==================================================
downloaded 58.4 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1297193 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 24.619   3.683  35.405 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
anacondaDownloadStats0.7820.0201.361
biocBuildReport5.1482.8856.910
biocDownloadStats2.5310.1443.235
biocMaintained1.1330.0161.424
biocPkgList0.8710.0661.302
biocPkgRanges000
biocRevDepEmail2.0740.0362.545
buildPkgDependencyDataFrame1.8980.0922.535
buildPkgDependencyIgraph0.9250.0201.057
class-dependencies4.7960.2044.999
firstInBioc4.2500.1234.860
generateBiocPkgDOI000
getBiocVignette1.5150.0561.998
get_bioc_data3.6870.1124.546
githubDetails1.0330.0411.385
githubURLParts0.8330.0491.253
inducedSubgraphByPkgs0.9150.0081.243
pkgCombDependencyGain4.6350.1085.660
pkgDepImports0.1760.0000.176
pkgDepMetrics4.3150.1095.297
pkgDownloadStats0.0380.0000.182
problemPage000
subgraphByDegree0.9530.0161.274