BioC 3.5: CHECK report for BiocGenerics on veracruz2

Package: BiocGenerics

Version: 0.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocGenerics_0.22.0.tar.gz

StartedAt: 2017-08-16 00:14:14 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:15:17 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 63.2 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_0.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BiocGenerics.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘0.22.0’
* 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'tapply':
tapply
  Code: function(X, INDEX, FUN = NULL, ..., default = NA, simplify =
                 TRUE)
  Docs: function(X, INDEX, FUN = NULL, ..., simplify = TRUE)
  Argument names in code not in docs:
    default
  Mismatches in argument names:
    Position: 5 Code: default Docs: simplify

Codoc mismatches from documentation object 'xtabs':
xtabs
  Code: function(formula = ˜., data = parent.frame(), subset, sparse =
                 FALSE, na.action, addNA = FALSE, exclude = if (!addNA)
                 c(NA, NaN), drop.unused.levels = FALSE)
  Docs: function(formula = ˜., data = parent.frame(), subset, sparse =
                 FALSE, na.action, exclude = c(NA, NaN),
                 drop.unused.levels = FALSE)
  Argument names in code not in docs:
    addNA
  Mismatches in argument names:
    Position: 6 Code: addNA Docs: exclude
    Position: 7 Code: exclude Docs: drop.unused.levels
  Mismatches in argument default values:
    Name: 'exclude' Code: if (!addNA) c(NA, NaN) Docs: c(NA, NaN)

* 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 8.811  0.033   9.074
plotMA      6.823  0.183   7.226
plotPCA     4.936  0.041   5.107
* 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-3.5-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	0.001	0.002
Extremes	0.013	0.002	0.015
IQR	0.002	0.000	0.002
annotation	0.201	0.008	0.219
append	0.006	0.000	0.006
as.data.frame	0.003	0.001	0.002
as.vector	0.002	0.000	0.002
boxplot	0.002	0.000	0.002
cbind	0.003	0.000	0.003
clusterApply	0.021	0.003	0.024
combine	0.199	0.002	0.203
dbconn	1.958	0.049	2.068
density	0.003	0.001	0.003
do.call	0.008	0.000	0.008
duplicated	0.004	0.001	0.005
eval	0.003	0.000	0.004
evalq	0.001	0.000	0.001
fileName	2.064	0.063	2.504
funprog	0.012	0.001	0.013
get	0.005	0.001	0.009
grep	0.003	0.000	0.003
image	0.002	0.001	0.002
is.unsorted	0.002	0.000	0.003
lapply	0.005	0.001	0.005
lengths	0.164	0.002	0.179
mad	0.002	0.000	0.002
mapply	0.001	0.000	0.002
match	0.003	0.000	0.003
matrix-summary	0.003	0.000	0.003
mean	0.003	0.001	0.003
normalize	0.034	0.001	0.035
nrow	0.010	0.001	0.011
order	0.005	0.001	0.005
organism_species	0.255	0.017	0.282
paste	0.002	0.000	0.002
plotMA	6.823	0.183	7.226
plotPCA	4.936	0.041	5.107
rank	0.005	0.001	0.004
relist	0.004	0.000	0.004
rep	0.004	0.001	0.003
residuals	0.002	0.000	0.003
row_colnames	0.010	0.001	0.011
score	0.099	0.003	0.103
sets	0.012	0.001	0.012
sort	0.003	0.000	0.004
start	0.089	0.004	0.095
strand	0.113	0.004	0.117
subset	0.038	0.002	0.040
t	0.005	0.000	0.006
table	0.003	0.000	0.003
tapply	0.004	0.000	0.005
testPackage	8.811	0.033	9.074
unique	0.002	0.000	0.004
unlist	0.004	0.000	0.003
unsplit	0.002	0.000	0.003
updateObject	0.302	0.005	0.309
var	0.002	0.000	0.003
weights	0.002	0.000	0.002
which	0.008	0.000	0.008
xtabs	0.004	0.001	0.004