Package: BiocPkgTools

Version: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2020-01-16 02:10:17 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:13:14 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 176.9 seconds

RetCode: 0

Status:  OK

CheckDir: BiocPkgTools.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiocPkgTools.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.5.0’
* 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 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 ... NOTE
inducedSubgraphByPkgs: warning in induced_subgraph(g, v = pkgs):
  partial argument match of 'v' to 'vids'
subgraphByDegree: warning in induced_subgraph(g, v = names(d2)):
  partial argument match of 'v' to 'vids'
.computeBiocViewsTransitiveClosure: no visible binding for global
  variable ‘biocViewsVocab’
biocBuildReport: no visible binding for global variable ‘start’
biocBuildReport: no visible global function definition for ‘capture’
biocBuildReport: no visible global function definition for
  ‘except_any_of’
biocBuildReport: no visible binding for global variable ‘blank’
biocBuildReport: no visible binding for global variable ‘anything’
biocBuildReport: no visible binding for global variable ‘any_alnums’
biocBuildReport: no visible global function definition for ‘maybe’
biocBuildReport: no visible binding for global variable ‘any_blanks’
biocBuildReport: no visible binding for global variable ‘any_alphas’
biocBuildReport: no visible binding for global variable
  ‘any_non_alnums’
biocBuildReport: no visible global function definition for ‘any_of’
biocBuildReport: no visible binding for global variable ‘digit’
biocDownloadStats: no visible binding for global variable ‘Year’
biocDownloadStats: no visible binding for global variable ‘Month’
firstInBioc: no visible binding for global variable ‘Month’
firstInBioc: no visible binding for global variable ‘Package’
firstInBioc: no visible global function definition for ‘desc’
firstInBioc: no visible binding for global variable ‘Date’
get_bioc_data: no visible binding for global variable ‘tags’
inducedSubgraphByPkgs: no visible global function definition for ‘V<-’
process_data: no visible binding for global variable ‘Author’
process_data: no visible binding for global variable ‘Package’
process_data: no visible binding for global variable ‘License’
process_data: no visible binding for global variable ‘biocViews’
process_data: no visible binding for global variable ‘Description’
process_data: no visible binding for global variable ‘downloads_month’
process_data: no visible binding for global variable ‘downloads_total’
summarise_dl_stats: no visible binding for global variable ‘Package’
summarise_dl_stats: no visible binding for global variable
  ‘Nb_of_downloads’
Undefined global functions or variables:
  Author Date Description License Month Nb_of_downloads Package V<-
  Year any_alnums any_alphas any_blanks any_non_alnums any_of anything
  biocViews biocViewsVocab blank capture desc digit downloads_month
  downloads_total except_any_of maybe start tags
Consider adding
  importFrom("stats", "start")
to your NAMESPACE file.
* 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
get_bioc_data               7.921  0.353   8.967
buildPkgDependencyDataFrame 6.741  0.390   7.452
biocBuildReport             3.655  1.721   5.972
buildPkgDependencyIgraph    5.007  0.249   5.531
inducedSubgraphByPkgs       4.912  0.229   5.398
subgraphByDegree            4.480  0.194   5.235
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiocPkgTools
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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/3.11/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1085942 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 18.629   5.111  24.771 

name	user	system	elapsed
biocBuildReport	3.655	1.721	5.972
biocDownloadStats	3.894	0.241	4.754
biocPkgList	2.292	0.123	2.933
buildPkgDependencyDataFrame	6.741	0.390	7.452
buildPkgDependencyIgraph	5.007	0.249	5.531
generateBiocPkgDOI	0	0	0
getBiocVignette	1.947	0.113	2.473
get_bioc_data	7.921	0.353	8.967
githubDetails	1.974	0.079	2.626
githubURLParts	1.920	0.072	2.161
inducedSubgraphByPkgs	4.912	0.229	5.398
problemPage	0.000	0.000	0.001
subgraphByDegree	4.480	0.194	5.235