Multiple platform build/check report for BioC 3.9 - CHECK report for biocViews on celaya2

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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_1.51.15.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/biocViews.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.51.15’
* 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 ... WARNING
Codoc mismatches from documentation object 'getPackageNEWS':
getPackageNEWS
  Code: function(prevRepos = "3.6", currRepos = "3.7", repo = c("bioc",
                 "data/experiment", "workflows"), srcdir = NULL)
  Docs: function(prevRepos = "3.6", currRepos = "3.7", repo = c("bioc",
                 "data/experiment", "workflows"))
  Argument names in code not in docs:
    srcdir

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'genReposControlFiles'
  ‘meatPath’
Documented arguments not in \usage in documentation object 'genReposControlFiles':
  ‘meanPath’

Undocumented arguments in documentation object 'write_VIEWS'
  ‘meatPath’
Documented arguments not in \usage in documentation object 'write_VIEWS':
  ‘type’ ‘meanPath’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/biocViews.Rcheck/00check.log’
for details.

Installation output

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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/3.6/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


R Under development (unstable) (2019-03-18 r76245) -- "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.

> BiocGenerics:::testPackage("biocViews")
WARNING: extractCitations
  tarball: /tmp/RtmpRD0JPe/testing/testrepos/src/contrib/biocViews_1.51.15.tar.gz
  warning: untar(compressed=) is deprecated
WARNING: extractCitations
  tarball: /tmp/RtmpRD0JPe/testing/testrepos/src/contrib/biocViews_1.51.15.tar.gz
  warning: untar(compressed=) is deprecated


RUNIT TEST PROTOCOL -- Tue Apr  9 00:13:53 2019 
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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 
  4.998   0.453   7.183

name	user	system	elapsed
PackageDetail-class	0.091	0.002	0.092
biocViews-package	0.058	0.003	0.062
biocViewsVocab	0.008	0.002	0.011
getBiocSubViews	1.185	0.013	1.209
getBiocViews	1.573	0.024	1.678
getCurrentbiocViews	0.014	0.000	0.015
getPackageTitles	0	0	0
getSubTerms	0.230	0.006	0.236
guessPackageType	0.028	0.000	0.028
recommendPackages	0.564	0.017	0.909
validation_tests	0.003	0.002	0.005

CHECK report for biocViews on celaya2

Summary

Command output

Installation output

Tests output

Example timings