BioC 3.6: CHECK report for BiocGenerics on tokay1

Package: BiocGenerics

Version: 0.23.0

Command: rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.23.0.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.23.0.tar.gz

StartedAt: 2017-08-15 21:59:05 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:00:48 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 102.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocGenerics.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.23.0.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.23.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocGenerics.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
testPackage 8.43   0.00    8.42
plotMA      5.86   0.11    6.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
testPackage 9.86   0.00    9.85
plotMA      6.69   0.15    6.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'BiocGenerics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocGenerics' as BiocGenerics_0.23.0.zip
* DONE (BiocGenerics)

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0	0	0
IQR	0.02	0.00	0.02
annotation	0.17	0.00	0.17
append	0.01	0.00	0.02
as.data.frame	0	0	0
as.vector	0	0	0
boxplot	0	0	0
cbind	0	0	0
clusterApply	0.02	0.00	0.01
combine	0.11	0.02	0.13
dbconn	1.70	0.05	1.75
density	0	0	0
do.call	0	0	0
duplicated	0	0	0
eval	0	0	0
evalq	0	0	0
fileName	2.40	0.07	2.81
funprog	0	0	0
get	0	0	0
grep	0	0	0
image	0	0	0
is.unsorted	0.01	0.00	0.01
lapply	0	0	0
lengths	0.35	0.02	0.36
mad	0	0	0
mapply	0	0	0
match	0	0	0
matrix-summary	0	0	0
mean	0	0	0
normalize	0.05	0.00	0.04
nrow	0.00	0.01	0.02
order	0	0	0
organism_species	0.33	0.03	0.36
paste	0	0	0
plotMA	5.86	0.11	6.39
plotPCA	4.44	0.04	4.48
rank	0.02	0.00	0.02
relist	0	0	0
rep	0	0	0
residuals	0	0	0
row_colnames	0.01	0.00	0.02
score	0.08	0.02	0.09
sets	0	0	0
sort	0.02	0.00	0.02
start	0.04	0.02	0.06
strand	0.10	0.00	0.09
subset	0.03	0.00	0.03
t	0	0	0
table	0	0	0
tapply	0.01	0.00	0.02
testPackage	8.43	0.00	8.42
unique	0	0	0
unlist	0	0	0
unsplit	0	0	0
updateObject	0.39	0.00	0.39
var	0	0	0
weights	0	0	0
which	0.02	0.00	0.01
xtabs	0	0	0

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0	0	0
IQR	0	0	0
annotation	0.21	0.00	0.21
append	0	0	0
as.data.frame	0	0	0
as.vector	0.02	0.00	0.02
boxplot	0	0	0
cbind	0	0	0
clusterApply	0.01	0.00	0.01
combine	0.16	0.00	0.16
dbconn	1.81	0.03	1.84
density	0	0	0
do.call	0	0	0
duplicated	0	0	0
eval	0	0	0
evalq	0	0	0
fileName	2.39	0.03	2.59
funprog	0	0	0
get	0	0	0
grep	0	0	0
image	0	0	0
is.unsorted	0	0	0
lapply	0	0	0
lengths	0.11	0.00	0.10
mad	0	0	0
mapply	0	0	0
match	0.01	0.00	0.02
matrix-summary	0.00	0.00	0.02
mean	0	0	0
normalize	0.03	0.00	0.03
nrow	0.00	0.01	0.02
order	0	0	0
organism_species	0.24	0.02	0.25
paste	0	0	0
plotMA	6.69	0.15	6.84
plotPCA	4.09	0.02	4.11
rank	0	0	0
relist	0	0	0
rep	0	0	0
residuals	0.02	0.00	0.02
row_colnames	0	0	0
score	0.09	0.00	0.09
sets	0	0	0
sort	0	0	0
start	0.06	0.00	0.06
strand	0.08	0.01	0.09
subset	0.04	0.00	0.05
t	0.02	0.00	0.02
table	0	0	0
tapply	0	0	0
testPackage	9.86	0.00	9.85
unique	0	0	0
unlist	0	0	0
unsplit	0	0	0
updateObject	0.25	0.02	0.27
var	0	0	0
weights	0	0	0
which	0.02	0.00	0.01
xtabs	0	0	0