BioC 3.2: CHECK report for BiocGenerics on moscato1

Package: BiocGenerics

Version: 0.15.6

Command: rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.15.6.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.15.6.tar.gz

StartedAt: 2015-08-20 01:49:43 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 01:51:33 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 110.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocGenerics.Rcheck

Warnings: 2

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### Running command:
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###   rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.15.6.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.15.6.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/BiocGenerics.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '0.15.6'
* 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 ... WARNING
Missing link or links in documentation object 'rank.Rd':
  '[S4Vectors]{rank,Vector-method}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'mad':
mad
  Code: function(x, center = median(x), constant = 1.4826, na.rm =
                 FALSE, low = FALSE, high = FALSE)
  Docs: function(x, center = median(x, na.rm = na.rm), constant =
                 1.4826, na.rm = FALSE, low = FALSE, high = FALSE)
  Mismatches in argument default values:
    Name: 'center' Code: median(x) Docs: median(x, na.rm = na.rm)

* 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' ... [27s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
plotMA   6.32   0.06    6.56
fileName 4.76   0.13    8.29
** running examples for arch 'x64' ... [27s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
testPackage 6.84   0.01    6.85
plotMA      6.41   0.09    6.94
fileName    5.51   0.05    7.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'BiocGenerics_unit_tests.R' [2s]
 [2s] OK
** running tests for arch 'x64' ...
  Running 'BiocGenerics_unit_tests.R' [2s]
 [2s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  'D:/biocbld/bbs-3.2-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 '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 'IQR' 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 'mad' 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 'rep.int' 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 '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_0.15.6.zip
* DONE (BiocGenerics)

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0.02	0.00	0.02
IQR	0	0	0
annotation	0.29	0.00	0.29
append	0	0	0
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	0.1	0.0	0.1
density	0	0	0
do.call	0	0	0
duplicated	0.01	0.00	0.01
eval	0	0	0
evalq	0	0	0
fileName	4.76	0.13	8.29
funprog	0.02	0.00	0.01
get	0	0	0
grep	0	0	0
image	0.01	0.00	0.02
is.unsorted	0	0	0
lapply	0	0	0
mad	0	0	0
mapply	0	0	0
match	0	0	0
normalize	0.03	0.00	0.03
nrow	0	0	0
order	0	0	0
organism_species	1	0	1
paste	0	0	0
plotMA	6.32	0.06	6.56
plotPCA	2.54	0.03	2.57
rank	0.01	0.00	0.02
relist	0	0	0
rep	0	0	0
residuals	0	0	0
row_colnames	0.02	0.00	0.02
score	0.11	0.01	0.12
sets	0.01	0.00	0.02
sort	0	0	0
start	0.07	0.02	0.07
strand	0.09	0.03	0.13
subset	0.03	0.00	0.04
table	0.01	0.00	0.01
tapply	0	0	0
testPackage	4.93	0.02	4.95
unique	0	0	0
unlist	0	0	0
unsplit	0	0	0
updateObject	0.2	0.0	0.2
weights	0.02	0.00	0.01
xtabs	0	0	0

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0.01	0.00	0.01
IQR	0	0	0
annotation	0.48	0.00	0.48
append	0	0	0
as.data.frame	0.02	0.00	0.01
as.vector	0	0	0
boxplot	0	0	0
cbind	0	0	0
clusterApply	0.03	0.00	0.03
combine	0.07	0.00	0.08
density	0	0	0
do.call	0	0	0
duplicated	0	0	0
eval	0.02	0.00	0.02
evalq	0	0	0
fileName	5.51	0.05	7.17
funprog	0.01	0.00	0.02
get	0.02	0.00	0.01
grep	0	0	0
image	0	0	0
is.unsorted	0.01	0.00	0.02
lapply	0	0	0
mad	0	0	0
mapply	0.02	0.00	0.01
match	0	0	0
normalize	0.06	0.00	0.07
nrow	0.02	0.00	0.01
order	0	0	0
organism_species	1.15	0.00	1.16
paste	0.02	0.00	0.01
plotMA	6.41	0.09	6.94
plotPCA	2.19	0.02	2.34
rank	0.01	0.00	0.02
relist	0	0	0
rep	0	0	0
residuals	0.02	0.00	0.01
row_colnames	0.00	0.01	0.02
score	0.14	0.00	0.14
sets	0	0	0
sort	0	0	0
start	0.09	0.00	0.09
strand	0.19	0.00	0.19
subset	0.06	0.00	0.06
table	0	0	0
tapply	0	0	0
testPackage	6.84	0.01	6.85
unique	0	0	0
unlist	0	0	0
unsplit	0	0	0
updateObject	0.28	0.00	0.28
weights	0	0	0
xtabs	0	0	0