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CHECK report for BiocPkgTools on merida1

This page was generated on 2020-04-15 12:48:01 -0400 (Wed, 15 Apr 2020).

Package 157/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.4.6
Sean Davis
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BiocPkgTools
Branch: RELEASE_3_10
Last Commit: 43e56c1
Last Changed Date: 2020-03-16 15:02:14 -0400 (Mon, 16 Mar 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocPkgTools
Version: 1.4.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocPkgTools_1.4.6.tar.gz
StartedAt: 2020-04-15 00:42:09 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:44:35 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 145.9 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocPkgTools_1.4.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/BiocPkgTools.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.6’
* 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 or elapsed time > 5s
                        user system elapsed
pkgCombDependencyGain 11.463  0.289  12.242
get_bioc_data          6.075  0.200   6.865
* 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-3.10-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.



Installation output

BiocPkgTools.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.org/packages/3.10/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1085869 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 22 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 14.757   2.341  17.979 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
biocBuildReport2.6030.7273.505
biocDownloadStats3.7230.1744.400
biocPkgList1.5910.0491.795
buildPkgDependencyDataFrame3.8760.0994.235
buildPkgDependencyIgraph2.4080.0562.601
firstInBioc4.2830.1904.894
generateBiocPkgDOI0.0000.0000.001
getBiocVignette1.6750.0512.031
get_bioc_data6.0750.2006.865
githubDetails1.4390.0531.822
githubURLParts1.4480.0411.616
inducedSubgraphByPkgs1.9040.0482.080
pkgCombDependencyGain11.463 0.28912.242
problemPage0.0010.0000.000
subgraphByDegree2.2260.0572.911