BioC 3.2: CHECK report for biocViews on zin1

Package: biocViews

Version: 1.37.11

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings biocViews_1.37.11.tar.gz

StartedAt: 2015-08-23 22:01:15 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:02:10 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 55.4 seconds

RetCode: 0

Status:  OK

CheckDir: biocViews.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings biocViews_1.37.11.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/biocViews.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.37.11’
* 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
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  inst/unitTests/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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
.getChildren: no visible binding for global variable ‘biocViewsVocab’
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 ... 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 ... [6s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [5s/9s]
 [5s/9s] 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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	0.081	0.000	0.080
biocViews-package	0.031	0.000	0.031
biocViewsVocab	0.004	0.000	0.004
getBiocSubViews	1.303	0.000	1.311
getBiocViews	1.282	0.000	1.282
getCurrentbiocViews	0.005	0.000	0.008
getSubTerms	0.126	0.000	0.126
recommendPackages	1.236	0.048	2.247
validation_tests	0.003	0.000	0.003