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CHECK report for BiocPkgTools on celaya2

This page was generated on 2020-01-16 13:52:15 -0500 (Thu, 16 Jan 2020).

Package 158/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.5.0
Sean Davis
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/BiocPkgTools
Branch: master
Last Commit: d401f77
Last Changed Date: 2019-10-29 13:43:19 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocPkgTools
Version: 1.5.0
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

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_1.5.0.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.



Installation output

BiocPkgTools.Rcheck/00install.out

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### Running command:
###
###   /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)

Tests output

BiocPkgTools.Rcheck/tests/testthat.Rout


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 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
biocBuildReport3.6551.7215.972
biocDownloadStats3.8940.2414.754
biocPkgList2.2920.1232.933
buildPkgDependencyDataFrame6.7410.3907.452
buildPkgDependencyIgraph5.0070.2495.531
generateBiocPkgDOI000
getBiocVignette1.9470.1132.473
get_bioc_data7.9210.3538.967
githubDetails1.9740.0792.626
githubURLParts1.9200.0722.161
inducedSubgraphByPkgs4.9120.2295.398
problemPage0.0000.0000.001
subgraphByDegree4.4800.1945.235