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This page was generated on 2021-10-25 14:06:50 -0400 (Mon, 25 Oct 2021).

CHECK results for BiocPkgTools on merida1

To the developers/maintainers of the BiocPkgTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocPkgTools.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 166/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.11.19  (landing page)
Sean Davis
Snapshot Date: 2021-10-24 14:50:04 -0400 (Sun, 24 Oct 2021)
git_url: https://git.bioconductor.org/packages/BiocPkgTools
git_branch: master
git_last_commit: 98326a2
git_last_commit_date: 2021-10-15 15:59:43 -0400 (Fri, 15 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: BiocPkgTools
Version: 1.11.19
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocPkgTools_1.11.19.tar.gz
StartedAt: 2021-10-25 01:05:00 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 01:10:59 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 358.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocPkgTools_1.11.19.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BiocPkgTools.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.11.19’
* 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       6.417 23.061  76.256
pkgCombDependencyGain 9.725  0.384  10.399
githubDetails         8.015  0.931   9.343
pkgDepMetrics         8.024  0.255   8.633
get_bioc_data         7.170  0.265   8.270
class-dependencies    6.849  0.203   7.062
firstInBioc           5.774  0.193   6.611
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.



Installation output

BiocPkgTools.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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.

> library(testthat)
> library(BiocPkgTools)
Loading required package: htmlwidgets
> 
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.riken.jp/checkResults/3.14/bioc-LATEST/report.tgz'
Content type 'application/x-gzip' length 57827367 bytes (55.1 MB)
==================================================
downloaded 55.1 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1297215 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 49.299  19.968  91.634 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
anacondaDownloadStats0.9690.0401.885
biocBuildReport 6.41723.06176.256
biocDownloadStats3.5640.1344.566
biocMaintained1.9530.0802.177
biocPkgList1.8100.0752.148
biocPkgRanges000
biocRevDepEmail3.3880.0903.972
buildPkgDependencyDataFrame3.7760.0874.275
buildPkgDependencyIgraph1.8510.0522.022
class-dependencies6.8490.2037.062
firstInBioc5.7740.1936.611
generateBiocPkgDOI000
getBiocVignette1.7340.1362.245
get_bioc_data7.1700.2658.270
githubDetails8.0150.9319.343
githubURLParts1.5880.0501.885
inducedSubgraphByPkgs1.7310.0491.891
pkgCombDependencyGain 9.725 0.38410.399
pkgDepImports0.3830.0110.396
pkgDepMetrics8.0240.2558.633
pkgDownloadStats0.0350.0010.219
problemPage000
subgraphByDegree1.7930.0572.121