BioC 3.5: CHECK report for BiocGenerics on veracruz2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocGenerics_0.22.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BiocGenerics.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.22.1’
* 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 ‘BiocGenerics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘graphics’ ‘stats’ ‘parallel’
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
'library' or 'require' call to ‘RUnit’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 ... OK
* 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 ... NOTE
S3 methods shown with full name in documentation object 'rep':
  ‘rep.int’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
testPackage 10.373  0.058  10.814
plotMA       7.488  0.231   7.942
plotPCA      5.027  0.052   5.265
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.

* installing *source* package ‘BiocGenerics’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’
Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
Creating a new generic function for ‘get’ in package ‘BiocGenerics’
Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
Creating a new generic function for ‘grep’ in package ‘BiocGenerics’
Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’
Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘lengths’ in package ‘BiocGenerics’
Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘match’ in package ‘BiocGenerics’
Creating a new generic function for ‘rowSums’ in package ‘BiocGenerics’
Creating a new generic function for ‘colSums’ in package ‘BiocGenerics’
Creating a new generic function for ‘rowMeans’ in package ‘BiocGenerics’
Creating a new generic function for ‘colMeans’ in package ‘BiocGenerics’
Creating a new generic function for ‘order’ in package ‘BiocGenerics’
Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
Creating a new generic function for ‘union’ in package ‘BiocGenerics’
Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’
Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’
Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
Creating a new generic function for ‘table’ in package ‘BiocGenerics’
Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’
Creating a new generic function for ‘var’ in package ‘BiocGenerics’
Creating a new generic function for ‘sd’ in package ‘BiocGenerics’
Creating a new generic function for ‘which’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’
Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’
Creating a new generic function for ‘mad’ in package ‘BiocGenerics’
Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterApply’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterApplyLB’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterEvalQ’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterExport’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’
Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’
Creating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BiocGenerics)

name	user	system	elapsed
BiocGenerics-package	0.002	0.000	0.002
Extremes	0.009	0.001	0.011
IQR	0.001	0.000	0.002
annotation	0.211	0.008	0.224
append	0.005	0.000	0.006
as.data.frame	0.002	0.000	0.002
as.vector	0.003	0.001	0.002
boxplot	0.002	0.000	0.002
cbind	0.002	0.001	0.003
clusterApply	0.020	0.002	0.023
combine	0.215	0.002	0.224
dbconn	2.091	0.061	2.213
density	0.002	0.001	0.002
do.call	0.001	0.000	0.002
duplicated	0.006	0.001	0.005
eval	0.003	0.000	0.003
evalq	0.001	0.000	0.000
fileName	2.168	0.069	2.590
funprog	0.008	0.001	0.010
get	0.004	0.000	0.005
grep	0.002	0.001	0.003
image	0.003	0.000	0.003
is.unsorted	0.002	0.001	0.003
lapply	0.003	0.000	0.004
lengths	0.300	0.003	0.314
mad	0.003	0.000	0.002
mapply	0.002	0.000	0.004
match	0.003	0.001	0.004
matrix-summary	0.002	0.000	0.002
mean	0.003	0.000	0.002
normalize	0.027	0.001	0.029
nrow	0.007	0.001	0.007
order	0.002	0.000	0.002
organism_species	0.294	0.022	0.329
paste	0.003	0.001	0.004
plotMA	7.488	0.231	7.942
plotPCA	5.027	0.052	5.265
rank	0.004	0.000	0.004
relist	0.003	0.001	0.004
rep	0.004	0.000	0.004
residuals	0.002	0.001	0.003
row_colnames	0.010	0.001	0.012
score	0.102	0.004	0.106
sets	0.010	0.001	0.013
sort	0.003	0.001	0.003
start	0.076	0.003	0.081
strand	0.112	0.004	0.118
subset	0.040	0.002	0.042
t	0.007	0.000	0.007
table	0.003	0.000	0.004
tapply	0.005	0.001	0.005
testPackage	10.373	0.058	10.814
unique	0.004	0.000	0.004
unlist	0.003	0.001	0.004
unsplit	0.002	0.000	0.003
updateObject	0.325	0.007	0.340
var	0.003	0.000	0.004
weights	0.003	0.001	0.003
which	0.008	0.000	0.009
xtabs	0.004	0.000	0.005

BioC 3.5: CHECK report for BiocGenerics on veracruz2

Summary

Command output