Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:05:01 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 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? 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 166/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.15.0  (landing page)
Sean Davis
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/BiocPkgTools
git_branch: master
git_last_commit: d6455b0
git_last_commit_date: 2022-04-26 11:50:55 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiocPkgTools
Version: 1.15.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings BiocPkgTools_1.15.0.tar.gz
StartedAt: 2022-06-23 18:54:32 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 18:56:58 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 145.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings BiocPkgTools_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/BiocPkgTools.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* 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 ‘1.15.0’
* 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 ‘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
class-dependencies    5.952  0.184   6.136
get_bioc_data         5.274  0.446   6.114
pkgCombDependencyGain 5.201  0.374   6.355
firstInBioc           5.139  0.292   5.510
* 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-3.16-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.



Installation output

BiocPkgTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL BiocPkgTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
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/packages/3.16/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1303785 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 26.060   3.772  30.321 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
anacondaDownloadStats0.8310.0081.428
biocBuildReport2.8321.1383.962
biocDownloadStats3.3460.1603.619
biocMaintained1.2000.0351.544
biocPkgList1.0000.0361.148
biocPkgRanges0.0000.0000.001
biocRevDepEmail1.0840.0241.680
buildPkgDependencyDataFrame2.3580.0712.823
buildPkgDependencyIgraph1.0250.0361.659
class-dependencies5.9520.1846.136
firstInBioc5.1390.2925.510
generateBiocPkgDOI0.0000.0000.001
getBiocVignette0.8100.0161.329
get_bioc_data5.2740.4466.114
githubDetails0.9570.0901.360
githubURLParts0.8230.0531.012
inducedSubgraphByPkgs1.0220.0481.186
pkgCombDependencyGain5.2010.3746.355
pkgDepImports0.1100.0030.113
pkgDepMetrics4.0280.1874.751
pkgDownloadStats0.0480.0000.199
problemPage000
subgraphByDegree0.9260.0481.096