BioC 3.6: CHECK report for BiocGenerics on veracruz1

Package: BiocGenerics

Version: 0.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocGenerics_0.23.0.tar.gz

StartedAt: 2017-08-16 00:25:17 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:26:38 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 80.9 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_0.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘0.23.0’
* 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 8.048  0.055   8.299
plotMA      6.886  0.177   7.229
* 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-3.6-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	0.001	0.000	0.002
Extremes	0.011	0.001	0.013
IQR	0.002	0.001	0.002
annotation	0.210	0.007	0.222
append	0.005	0.001	0.005
as.data.frame	0.002	0.000	0.002
as.vector	0.002	0.000	0.003
boxplot	0.001	0.000	0.002
cbind	0.003	0.000	0.004
clusterApply	0.026	0.002	0.028
combine	0.187	0.003	0.197
dbconn	1.974	0.049	2.052
density	0.003	0.000	0.003
do.call	0.003	0.000	0.002
duplicated	0.004	0.000	0.005
eval	0.002	0.000	0.002
evalq	0	0	0
fileName	2.478	0.067	2.927
funprog	0.010	0.002	0.012
get	0.004	0.000	0.005
grep	0.003	0.001	0.003
image	0.002	0.000	0.002
is.unsorted	0.003	0.000	0.003
lapply	0.003	0.000	0.004
lengths	0.097	0.010	0.108
mad	0.002	0.000	0.003
mapply	0.002	0.000	0.003
match	0.003	0.001	0.003
matrix-summary	0.002	0.000	0.003
mean	0.002	0.001	0.003
normalize	0.027	0.001	0.029
nrow	0.008	0.001	0.008
order	0.004	0.001	0.005
organism_species	0.265	0.010	0.290
paste	0.003	0.001	0.003
plotMA	6.886	0.177	7.229
plotPCA	4.264	0.042	4.425
rank	0.004	0.000	0.004
relist	0.004	0.001	0.004
rep	0.003	0.000	0.003
residuals	0.002	0.000	0.003
row_colnames	0.011	0.001	0.013
score	0.101	0.003	0.109
sets	0.009	0.001	0.011
sort	0.003	0.000	0.004
start	0.070	0.002	0.074
strand	0.093	0.003	0.100
subset	0.034	0.001	0.035
t	0.006	0.000	0.006
table	0.003	0.001	0.003
tapply	0.003	0.000	0.004
testPackage	8.048	0.055	8.299
unique	0.004	0.000	0.004
unlist	0.004	0.001	0.004
unsplit	0.003	0.000	0.003
updateObject	0.307	0.006	0.323
var	0.004	0.000	0.004
weights	0.002	0.001	0.002
which	0.009	0.001	0.010
xtabs	0.007	0.000	0.010