BioC 3.4: CHECK report for BiocGenerics on morelia

Package: BiocGenerics

Version: 0.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocGenerics_0.20.0.tar.gz

StartedAt: 2017-04-14 23:10:39 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:11:33 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 54.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocGenerics.Rcheck

Warnings: 1

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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_0.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BiocGenerics.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.20.0’
* 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 ... WARNING
Missing link or links in documentation object 'sets.Rd':
  ‘[GenomicRanges]{union,GRanges,GRanges-method}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 7.130  0.008   7.143
plotMA      6.083  0.168   6.263
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-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 ‘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 ‘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	0.001	0.000	0.003
Extremes	0.010	0.001	0.011
IQR	0.002	0.000	0.002
annotation	0.235	0.007	0.241
append	0.003	0.000	0.003
as.data.frame	0.002	0.001	0.003
as.vector	0.001	0.000	0.002
boxplot	0.002	0.000	0.001
cbind	0.002	0.001	0.003
clusterApply	0.017	0.001	0.018
combine	0.055	0.001	0.057
dbconn	2.219	0.044	2.264
density	0.004	0.000	0.004
do.call	0.003	0.000	0.003
duplicated	0.005	0.000	0.005
eval	0.002	0.000	0.003
evalq	0.001	0.000	0.000
fileName	2.457	0.075	2.827
funprog	0.011	0.001	0.013
get	0.004	0.000	0.005
grep	0.003	0.001	0.003
image	0.002	0.000	0.002
is.unsorted	0.002	0.000	0.003
lapply	0.005	0.000	0.005
lengths	0.055	0.005	0.059
mad	0.003	0.000	0.004
mapply	0.002	0.001	0.003
match	0.004	0.001	0.005
normalize	0.031	0.002	0.035
nrow	0.011	0.002	0.012
order	0.004	0.001	0.004
organism_species	0.341	0.011	0.353
paste	0.004	0.000	0.003
plotMA	6.083	0.168	6.263
plotPCA	2.289	0.017	2.311
rank	0.004	0.000	0.005
relist	0.003	0.000	0.003
rep	0.004	0.001	0.004
residuals	0.002	0.000	0.003
row_colnames	0.016	0.002	0.017
score	0.114	0.003	0.117
sets	0.013	0.001	0.013
sort	0.004	0.001	0.004
start	0.082	0.003	0.085
strand	0.117	0.004	0.122
subset	0.048	0.001	0.050
table	0.004	0.000	0.004
tapply	0.004	0.001	0.005
testPackage	7.130	0.008	7.143
unique	0.004	0.000	0.004
unlist	0.004	0.001	0.005
unsplit	0.002	0.000	0.003
updateObject	0.214	0.006	0.221
weights	0.003	0.001	0.003
which	0.01	0.00	0.01
xtabs	0.004	0.000	0.004