Package: biocViews

Version: 1.50.10

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:biocViews.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings biocViews_1.50.10.tar.gz

StartedAt: 2019-04-15 22:30:24 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:31:18 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 54.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: biocViews.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:biocViews.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings biocViews_1.50.10.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/biocViews.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/biocViews.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL biocViews
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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-pc-linux-gnu (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 22:31:15 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 
  3.664   0.192   5.783 

name	user	system	elapsed
PackageDetail-class	0.092	0.000	0.090
biocViews-package	0.056	0.000	0.055
biocViewsVocab	0.004	0.000	0.006
getBiocSubViews	1.276	0.000	1.310
getBiocViews	1.164	0.004	1.171
getCurrentbiocViews	0.008	0.000	0.007
getPackageTitles	0	0	0
getSubTerms	0.132	0.000	0.131
guessPackageType	0.012	0.000	0.013
recommendPackages	0.444	0.016	1.041
validation_tests	0.004	0.000	0.003