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This page was generated on 2021-10-25 14:06:50 -0400 (Mon, 25 Oct 2021).

CHECK results for biocViews on merida1

To the developers/maintainers of the biocViews package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biocViews.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 173/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocViews 1.61.3  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-10-24 14:50:04 -0400 (Sun, 24 Oct 2021)
git_url: https://git.bioconductor.org/packages/biocViews
git_branch: master
git_last_commit: 3b25b04
git_last_commit_date: 2021-10-18 17:48:28 -0400 (Mon, 18 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: biocViews
Version: 1.61.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biocViews.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biocViews_1.61.3.tar.gz
StartedAt: 2021-10-25 01:07:02 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 01:08:34 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 92.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biocViews.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biocViews.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biocViews_1.61.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/biocViews.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biocViews/DESCRIPTION’ ... OK
* this is package ‘biocViews’ version ‘1.61.3’
* 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 ‘biocViews’ 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
':::' call which should be '::': ‘tools:::vignetteInfo’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘tools:::.build_news_db_from_package_NEWS_Rd’
  ‘tools:::.build_news_db_from_package_NEWS_md’
  ‘tools:::.build_repository_package_db’
  ‘tools:::.get_standard_repository_db_fields’
  ‘tools:::.news_reader_default’ ‘tools:::.split_dependencies’
  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
getPackageNEWS : getNews: no visible binding for global variable
  ‘Version’
getReverseDepends : <anonymous>: no visible binding for global variable
  ‘Package’
Undefined global functions or variables:
  Package Version
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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-3.14-bioc/meat/biocViews.Rcheck/00check.log’
for details.



Installation output

biocViews.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biocViews
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘biocViews’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘HOWTO-BCV.Rnw’ 
   ‘createReposHtml.Rnw’ 
** 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 (biocViews)

Tests output

biocViews.Rcheck/tests/runTests.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> BiocGenerics:::testPackage("biocViews")
Generate citation for /tmp/RtmpkVTEeg/testing/testrepos/src/contrib/biocViews2_1.61.3.tar.gz ... (try to process CITATION file) OK
Generate citation for /tmp/RtmpkVTEeg/testing/testrepos/src/contrib/biocViews_1.61.3.tar.gz ... tar: biocViews/inst/CITATION: Not found in archive
tar: Error exit delayed from previous errors.
(auto-generate from DESCRIPTION file) OK


RUNIT TEST PROTOCOL -- Mon Oct 25 01:08:24 2021 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
biocViews RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
Warning message:
In untar(tarball, tpaths, exdir = tmpdir) :
  '/usr/bin/tar -xf '/tmp/RtmpkVTEeg/testing/testrepos/src/contrib/biocViews_1.61.3.tar.gz' -C '/tmp/RtmpkVTEeg' 'biocViews/DESCRIPTION' 'biocViews/inst/CITATION'' returned error code 1
> 
> proc.time()
   user  system elapsed 
  6.127   0.370   8.179 

Example timings

biocViews.Rcheck/biocViews-Ex.timings

nameusersystemelapsed
PackageDetail-class0.1120.0010.114
biocViews-package0.0750.0020.078
biocViewsVocab0.0050.0020.007
getBiocSubViews1.7670.0511.823
getBiocViews1.3900.0121.405
getCurrentbiocViews0.0150.0010.017
getPackageTitles0.0010.0000.001
getSubTerms0.2430.0030.245
guessPackageType0.0190.0000.019
recommendPackages0.8310.0201.213
validation_tests0.0040.0020.007