BioC 3.5: CHECK report for variancePartition on malbec2

Package: variancePartition

Version: 1.6.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.6.0.tar.gz

StartedAt: 2017-08-16 02:50:07 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:54:22 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 254.8 seconds

RetCode: 0

Status:  OK

CheckDir: variancePartition.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/variancePartition.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.6.0’
* 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 ‘variancePartition’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
fitVarPartModel-method         22.068  0.864  42.357
extractVarPart                 13.712  0.444  27.841
getVarianceComponents           4.680  0.756  14.585
varPartConfInf                  3.840  0.484  17.606
residuals-VarParFitList-method  3.404  0.592  13.387
fitExtractVarPartModel-method   1.440  0.232  20.185
plotCorrStructure               1.132  0.364   6.829
plotPercentBars                 1.064  0.392  12.087
sortCols-method                 0.612  0.324  11.725
plotVarPart-method              0.584  0.332  11.712
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘variancePartition’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (variancePartition)

name	user	system	elapsed
ESS-method	0.740	0.020	0.929
as.matrix-varPartResults-method	1.344	0.000	1.348
calcVarPart-method	0.124	0.000	0.123
canCorPairs	0.256	0.004	0.259
colinearityScore	0.852	0.000	0.856
extractVarPart	13.712	0.444	27.841
fitExtractVarPartModel-method	1.440	0.232	20.185
fitVarPartModel-method	22.068	0.864	42.357
getVarianceComponents	4.680	0.756	14.585
ggColorHue	0.000	0.000	0.001
plotCorrMatrix	0.468	0.000	0.467
plotCorrStructure	1.132	0.364	6.829
plotPercentBars	1.064	0.392	12.087
plotStratify	0.948	0.080	1.031
plotStratifyBy	0.692	0.040	0.734
plotVarPart-method	0.584	0.332	11.712
residuals-VarParFitList-method	3.404	0.592	13.387
sortCols-method	0.612	0.324	11.725
varPartConfInf	3.840	0.484	17.606