BioC 3.2: CHECK report for BiocGenerics on perceval

Package: BiocGenerics

Version: 0.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocGenerics_0.16.1.tar.gz

StartedAt: 2015-11-10 02:33:05 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:34:06 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 61.5 seconds

RetCode: 0

Status:  OK

CheckDir: BiocGenerics.Rcheck

Warnings: 0

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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_0.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/BiocGenerics.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.16.1’
* 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 ... [3s/4s] 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 ... [24s/24s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
testPackage 6.753  0.004   6.757
plotMA      5.618  0.102   5.775
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘BiocGenerics_unit_tests.R’ [2s/2s]
 [2s/2s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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 ‘as.vector’ 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 ‘unlist’ in package ‘BiocGenerics’
Creating a new generic function for ‘unsplit’ 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	0.010	0.001	0.011
IQR	0.002	0.000	0.002
annotation	0.321	0.007	0.327
append	0.003	0.000	0.003
as.data.frame	0.002	0.000	0.002
as.vector	0.002	0.000	0.002
boxplot	0.002	0.000	0.003
cbind	0.003	0.000	0.004
clusterApply	0.025	0.002	0.028
combine	0.077	0.002	0.079
dbconn	2.634	0.050	2.685
density	0.003	0.001	0.003
do.call	0.003	0.000	0.003
duplicated	0.005	0.001	0.006
eval	0.003	0.000	0.004
evalq	0.001	0.000	0.001
fileName	3.206	0.083	3.291
funprog	0.011	0.001	0.012
get	0.005	0.000	0.005
grep	0.003	0.001	0.002
image	0.002	0.000	0.002
is.unsorted	0.002	0.000	0.002
lapply	0.006	0.001	0.006
lengths	0.095	0.001	0.097
mad	0.003	0.000	0.003
mapply	0.002	0.001	0.003
match	0.004	0.000	0.004
normalize	0.077	0.001	0.079
nrow	0.011	0.001	0.011
order	0.003	0.000	0.004
organism_species	0.425	0.026	0.451
paste	0.003	0.001	0.003
plotMA	5.618	0.102	5.775
plotPCA	2.142	0.016	2.159
rank	0.005	0.000	0.005
relist	0.003	0.000	0.004
rep	0.003	0.001	0.004
residuals	0.002	0.000	0.002
row_colnames	0.013	0.002	0.014
score	0.234	0.012	0.245
sets	0.010	0.001	0.010
sort	0.003	0.001	0.003
start	0.148	0.003	0.151
strand	0.234	0.004	0.238
subset	0.079	0.001	0.081
table	0.003	0.001	0.003
tapply	0.003	0.000	0.004
testPackage	6.753	0.004	6.757
unique	0.004	0.000	0.004
unlist	0.004	0.000	0.004
unsplit	0.003	0.000	0.003
updateObject	0.252	0.007	0.260
weights	0.002	0.000	0.003
xtabs	0.005	0.000	0.005