BioC 3.5: CHECK report for BiocGenerics on tokay2

Package: BiocGenerics

Version: 0.22.1

Command: rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.22.1.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.22.1.tar.gz

StartedAt: 2017-10-17 22:18:50 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:20:42 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 112.0 seconds

RetCode: 0

Status:  OK

CheckDir: BiocGenerics.Rcheck

Warnings: 0

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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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.22.1.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.22.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BiocGenerics.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '0.22.1'
* 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 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
testPackage 8.26   0.01    8.28
plotMA      7.16   0.30    7.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
testPackage 11.69   0.00   11.71
plotMA       6.57   0.23    6.81
plotPCA      5.15   0.00    5.14
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-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_0.22.1.zip
* DONE (BiocGenerics)

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0	0	0
IQR	0	0	0
annotation	0.17	0.00	0.17
append	0	0	0
as.data.frame	0.01	0.00	0.02
as.vector	0	0	0
boxplot	0	0	0
cbind	0	0	0
clusterApply	0.02	0.00	0.01
combine	0.14	0.00	0.15
dbconn	1.56	0.03	1.59
density	0	0	0
do.call	0	0	0
duplicated	0.02	0.00	0.01
eval	0	0	0
evalq	0	0	0
fileName	1.81	0.11	2.04
funprog	0	0	0
get	0.02	0.00	0.01
grep	0	0	0
image	0	0	0
is.unsorted	0	0	0
lapply	0	0	0
lengths	0.15	0.00	0.16
mad	0	0	0
mapply	0	0	0
match	0	0	0
matrix-summary	0.00	0.00	0.02
mean	0	0	0
normalize	0.03	0.00	0.03
nrow	0.01	0.00	0.02
order	0	0	0
organism_species	0.49	0.01	0.50
paste	0	0	0
plotMA	7.16	0.30	7.53
plotPCA	3.79	0.02	3.81
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	0.08	0.00	0.07
sets	0	0	0
sort	0	0	0
start	0.05	0.01	0.06
strand	0.08	0.02	0.10
subset	0.03	0.00	0.03
t	0.02	0.00	0.02
table	0	0	0
tapply	0	0	0
testPackage	8.26	0.01	8.28
unique	0.02	0.00	0.01
unlist	0	0	0
unsplit	0	0	0
updateObject	0.23	0.00	0.24
var	0	0	0
weights	0.02	0.00	0.01
which	0	0	0
xtabs	0	0	0

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0.02	0.00	0.01
IQR	0	0	0
annotation	0.21	0.00	0.22
append	0.02	0.00	0.01
as.data.frame	0	0	0
as.vector	0	0	0
boxplot	0	0	0
cbind	0	0	0
clusterApply	0.02	0.00	0.02
combine	0.18	0.00	0.19
dbconn	2.00	0.07	2.06
density	0	0	0
do.call	0.02	0.00	0.01
duplicated	0	0	0
eval	0	0	0
evalq	0	0	0
fileName	2.28	0.07	2.49
funprog	0.02	0.00	0.01
get	0	0	0
grep	0	0	0
image	0	0	0
is.unsorted	0.01	0.00	0.02
lapply	0	0	0
lengths	0.11	0.00	0.11
mad	0	0	0
mapply	0	0	0
match	0	0	0
matrix-summary	0.02	0.00	0.05
mean	0	0	0
normalize	0.03	0.00	0.03
nrow	0.28	0.00	0.28
order	0	0	0
organism_species	0.28	0.04	0.31
paste	0	0	0
plotMA	6.57	0.23	6.81
plotPCA	5.15	0.00	5.14
rank	0	0	0
relist	0	0	0
rep	0	0	0
residuals	0	0	0
row_colnames	0.02	0.00	0.01
score	0.11	0.00	0.11
sets	0	0	0
sort	0.01	0.00	0.02
start	0.06	0.00	0.06
strand	0.07	0.02	0.08
subset	0.03	0.00	0.03
t	0.01	0.00	0.01
table	0	0	0
tapply	0	0	0
testPackage	11.69	0.00	11.71
unique	0	0	0
unlist	0	0	0
unsplit	0	0	0
updateObject	0.28	0.00	0.28
var	0	0	0
weights	0	0	0
which	0.02	0.00	0.01
xtabs	0	0	0