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CHECK report for BiocPkgTools on malbec1

This page was generated on 2020-08-12 11:22:25 -0400 (Wed, 12 Aug 2020).

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 158/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.7.0
Sean Davis
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/BiocPkgTools
Branch: master
Last Commit: 153abf3
Last Changed Date: 2020-04-27 15:19:21 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocPkgTools
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2020-08-12 05:29:39 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 05:32:10 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 151.1 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiocPkgTools.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.7.0’
* 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
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
pkgCombDependencyGain 9.792  0.044  10.175
pkgDepMetrics         9.444  0.064   9.908
get_bioc_data         7.712  0.048   8.418
* 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 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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 1331895 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 22 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 12.772   0.816  14.765 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
biocBuildReport1.7080.3282.309
biocDownloadStats4.1120.0364.667
biocPkgList1.5640.0201.821
buildPkgDependencyDataFrame3.5480.0043.885
buildPkgDependencyIgraph1.9320.0082.098
firstInBioc4.3720.0164.913
generateBiocPkgDOI000
getBiocVignette1.3880.0241.785
get_bioc_data7.7120.0488.418
githubDetails1.8080.0282.161
githubURLParts1.5280.0161.702
inducedSubgraphByPkgs2.0320.0122.232
pkgCombDependencyGain 9.792 0.04410.175
pkgDepImports0.2000.0000.198
pkgDepMetrics9.4440.0649.908
problemPage000
subgraphByDegree1.7920.0081.960