Package: biocViews

Version: 1.50.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biocViews.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biocViews_1.50.10.tar.gz

StartedAt: 2019-04-15 22:36:27 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:37:31 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 63.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: biocViews.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biocViews.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biocViews_1.50.10.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/biocViews.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biocViews/DESCRIPTION’ ... OK
* this is package ‘biocViews’ version ‘1.50.10’
* 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
Unexported objects imported by ':::' calls:
  ‘tools:::.build_news_db_from_package_NEWS_Rd’
  ‘tools:::.build_repository_package_db’
  ‘tools:::.get_standard_repository_db_fields’
  ‘tools:::.news_reader_default’ ‘tools:::.split_dependencies’
  ‘tools:::vignetteInfo’
  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 ... WARNING
Codoc mismatches from documentation object 'genReposControlFiles':
genReposControlFiles
  Code: function(reposRoot, contribPaths, manifestFile = NA, meatPath =
                 NA)
  Docs: function(reposRoot, contribPaths)
  Argument names in code not in docs:
    manifestFile meatPath

Codoc mismatches from documentation object 'write_VIEWS':
write_VIEWS
  Code: function(reposRootPath, fields = NULL, verbose = FALSE,
                 vignette.dir = "vignettes", manifestFile = NA,
                 meatPath = NA)
  Docs: function(reposRootPath, fields = NULL, type = c("source",
                 "win.binary", "mac.binary", "mac.binary.mavericks",
                 "mac.binary.el-capitan"), verbose = FALSE,
                 vignette.dir = "vignettes")
  Argument names in code not in docs:
    manifestFile meatPath
  Argument names in docs not in code:
    type
  Mismatches in argument names:
    Position: 3 Code: verbose Docs: type
    Position: 4 Code: vignette.dir Docs: verbose
    Position: 5 Code: manifestFile Docs: vignette.dir

* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/biocViews.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 biocViews
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘biocViews’ ...
** 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
* DONE (biocViews)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> BiocGenerics:::testPackage("biocViews")


RUNIT TEST PROTOCOL -- Mon Apr 15 22:37:24 2019 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
  4.525   0.275   5.910 

name	user	system	elapsed
PackageDetail-class	0.100	0.001	0.103
biocViews-package	0.056	0.001	0.057
biocViewsVocab	0.006	0.001	0.008
getBiocSubViews	1.216	0.005	1.237
getBiocViews	1.176	0.010	1.197
getCurrentbiocViews	0.013	0.001	0.013
getPackageTitles	0.000	0.000	0.001
getSubTerms	0.191	0.003	0.195
guessPackageType	0.022	0.001	0.024
recommendPackages	0.514	0.015	0.811
validation_tests	0.003	0.001	0.004