BioC 3.3: CHECK report for variancePartition on oaxaca

Package: variancePartition

Version: 1.2.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.2.11.tar.gz

StartedAt: 2016-10-13 07:05:47 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:10:12 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 265.6 seconds

RetCode: 0

Status:  OK

CheckDir: variancePartition.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.2.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/variancePartition.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.2.11’
* 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 sizes of PDF files under ‘inst/doc’ ... 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         23.377  1.493  39.291
extractVarPart                 13.363  0.680  28.089
varPartConfInf                  5.950  0.379  23.175
getVarianceComponents           4.321  0.472  10.766
residuals-VarParFitList-method  2.736  0.293   9.327
fitExtractVarPartModel-method   1.194  0.090  23.614
plotCorrStructure               1.124  0.040   6.334
plotPercentBars                 0.939  0.031  11.396
plotVarPart-method              0.882  0.034  10.973
sortCols-method                 0.698  0.031  10.245
* 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	0.243	0.005	0.275
calcVarPart-method	0.102	0.002	0.104
canCorPairs	0.064	0.004	0.068
colinearityScore	0.688	0.015	0.703
extractVarPart	13.363	0.680	28.089
fitExtractVarPartModel-method	1.194	0.090	23.614
fitVarPartModel-method	23.377	1.493	39.291
getVarianceComponents	4.321	0.472	10.766
ggColorHue	0.001	0.000	0.001
plotCorrMatrix	0.093	0.004	0.097
plotCorrStructure	1.124	0.040	6.334
plotPercentBars	0.939	0.031	11.396
plotStratify	0.966	0.003	0.969
plotStratifyBy	0.963	0.009	0.973
plotVarPart-method	0.882	0.034	10.973
residuals-VarParFitList-method	2.736	0.293	9.327
sortCols-method	0.698	0.031	10.245
varPartConfInf	5.950	0.379	23.175