BioC 2.14: CHECK report for biocViews on zin2

Package: biocViews

Version: 1.32.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings biocViews_1.32.1.tar.gz

StartedAt: 2014-10-07 22:05:06 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:05:58 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 51.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: biocViews.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings biocViews_1.32.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/biocViews.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biocViews/DESCRIPTION’ ... OK
* this is package ‘biocViews’ version ‘1.32.1’
* 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 ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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’
validate_bioc_views: no visible binding for global variable
  ‘biocViewsVocab’
htmlDoc,BiocView: no visible binding for global variable ‘stylesheet’
* 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 'write_VIEWS':
write_VIEWS
  Code: function(reposRootPath, fields = NULL, type = c("source",
                 "win.binary", "win64.binary", "mac.binary",
                 "mac.binary.leopard", "mac.binary.mavericks"), verbose
                 = FALSE, vignette.dir = "vignettes")
  Docs: function(reposRootPath, fields = NULL, type = c("source",
                 "win.binary", "win64.binary", "mac.binary",
                 "mac.binary.leopard"), verbose = FALSE, vignette.dir =
                 "vignettes")
  Mismatches in argument default values:
    Name: 'type'
    Code: c("source", "win.binary", "win64.binary", "mac.binary", "mac.binary.leopard", 
          "mac.binary.mavericks")
    Docs: c("source", "win.binary", "win64.binary", "mac.binary", "mac.binary.leopard")

* 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 ... [5s/5s] 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/biocViews.Rcheck/00check.log’
for details.

* installing *source* package ‘biocViews’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biocViews)

name	user	system	elapsed
PackageDetail-class	0.108	0.000	0.108
biocViews-package	0.028	0.000	0.029
biocViewsVocab	0.008	0.000	0.006
getBiocSubViews	1.260	0.004	1.268
getBiocViews	1.176	0.000	1.180
getSubTerms	0.100	0.000	0.101
validation_tests	0.004	0.000	0.004