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CHECK report for BiocPkgTools on malbec1

This page was generated on 2021-05-06 12:26:59 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the BiocPkgTools package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 167/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.8.2  (landing page)
Sean Davis
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/BiocPkgTools
Branch: RELEASE_3_12
Last Commit: f427c50
Last Changed Date: 2021-04-13 15:30:49 -0400 (Tue, 13 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: BiocPkgTools
Version: 1.8.2
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiocPkgTools_1.8.2.tar.gz
StartedAt: 2021-05-05 23:27:22 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:30:15 -0400 (Wed, 05 May 2021)
EllapsedTime: 173.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiocPkgTools_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiocPkgTools.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.8.2’
* 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
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘BiocManager:::.repositories’
  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       12.956  0.136  13.452
pkgCombDependencyGain 11.252  0.052  11.749
pkgDepMetrics         11.000  0.032  11.455
get_bioc_data          5.756  0.052   6.640
firstInBioc            4.860  0.040   5.587
biocDownloadStats      4.332  0.048   5.114
* 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-3.12-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.



Installation output

BiocPkgTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BiocPkgTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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/3.12/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1312841 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
 19.188   0.304  20.907 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
biocBuildReport12.956 0.13613.452
biocDownloadStats4.3320.0485.114
biocPkgList1.6840.0081.971
buildPkgDependencyDataFrame3.5560.0364.018
buildPkgDependencyIgraph1.9400.0082.255
firstInBioc4.8600.0405.587
generateBiocPkgDOI000
getBiocVignette1.6800.0162.401
get_bioc_data5.7560.0526.640
githubDetails1.6840.2844.850
githubURLParts1.8080.0682.070
inducedSubgraphByPkgs1.9400.0082.183
pkgCombDependencyGain11.252 0.05211.749
pkgDepImports0.1360.0000.136
pkgDepMetrics11.000 0.03211.455
problemPage000
subgraphByDegree1.7000.0161.917