BioC 3.5: CHECK report for BiocGenerics on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings BiocGenerics_0.22.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/BiocGenerics.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 10.364  0.004  10.375
plotMA       5.936  0.064   6.030
* 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
  ‘/home/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	0.000	0.000	0.001
Extremes	0.004	0.000	0.007
IQR	0.000	0.000	0.002
annotation	0.196	0.000	0.196
append	0.000	0.000	0.002
as.data.frame	0.000	0.000	0.002
as.vector	0.004	0.000	0.001
boxplot	0.000	0.000	0.002
cbind	0.004	0.000	0.002
clusterApply	0.016	0.000	0.017
combine	0.168	0.004	0.169
dbconn	1.684	0.020	1.706
density	0.008	0.000	0.007
do.call	0.000	0.000	0.002
duplicated	0.000	0.004	0.003
eval	0.000	0.000	0.002
evalq	0.000	0.000	0.001
fileName	2.020	0.024	2.547
funprog	0.004	0.000	0.006
get	0.000	0.000	0.003
grep	0.004	0.000	0.001
image	0.000	0.000	0.002
is.unsorted	0.000	0.000	0.002
lapply	0.004	0.000	0.003
lengths	0.120	0.004	0.124
mad	0.000	0.000	0.002
mapply	0.004	0.000	0.001
match	0.004	0.000	0.002
matrix-summary	0.000	0.000	0.002
mean	0.004	0.000	0.002
normalize	0.024	0.000	0.022
nrow	0.008	0.000	0.006
order	0.000	0.000	0.003
organism_species	0.416	0.008	0.426
paste	0.004	0.000	0.004
plotMA	5.936	0.064	6.030
plotPCA	3.988	0.012	4.004
rank	0.004	0.000	0.004
relist	0.004	0.000	0.002
rep	0.004	0.000	0.002
residuals	0.000	0.000	0.001
row_colnames	0.008	0.000	0.008
score	0.076	0.000	0.076
sets	0.008	0.000	0.007
sort	0.004	0.000	0.003
start	0.056	0.000	0.054
strand	0.060	0.008	0.071
subset	0.020	0.000	0.021
t	0.004	0.000	0.005
table	0.000	0.000	0.002
tapply	0.000	0.000	0.002
testPackage	10.364	0.004	10.375
unique	0.004	0.000	0.002
unlist	0.004	0.000	0.002
unsplit	0.000	0.000	0.002
updateObject	0.236	0.004	0.238
var	0.004	0.000	0.003
weights	0.000	0.000	0.002
which	0.008	0.000	0.006
xtabs	0.000	0.000	0.003

BioC 3.5: CHECK report for BiocGenerics on malbec2

Summary

Command output