BioC 3.5: CHECK report for variancePartition on oaxaca

Package: variancePartition

Version: 1.5.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.5.7.tar.gz

StartedAt: 2017-03-04 10:19:50 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 10:24:31 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 281.5 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_1.5.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/variancePartition.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.5.7’
* 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         22.611  1.600  36.863
extractVarPart                 12.820  0.678  25.816
varPartConfInf                  6.064  0.040  25.349
getVarianceComponents           4.840  0.914  13.994
residuals-VarParFitList-method  3.322  0.339  12.117
plotPercentBars                 1.662  0.053  14.663
plotCorrStructure               1.646  0.057   9.241
fitExtractVarPartModel-method   1.569  0.078  23.528
sortCols-method                 0.811  0.032  14.313
plotVarPart-method              0.700  0.027  13.927
* 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	0.828	0.018	0.906
as.matrix-varPartResults-method	1.528	0.003	1.531
calcVarPart-method	0.181	0.002	0.184
canCorPairs	0.312	0.004	0.316
colinearityScore	0.618	0.004	0.623
extractVarPart	12.820	0.678	25.816
fitExtractVarPartModel-method	1.569	0.078	23.528
fitVarPartModel-method	22.611	1.600	36.863
getVarianceComponents	4.840	0.914	13.994
ggColorHue	0.001	0.000	0.000
plotCorrMatrix	0.836	0.015	0.864
plotCorrStructure	1.646	0.057	9.241
plotPercentBars	1.662	0.053	14.663
plotStratify	1.322	0.009	1.338
plotStratifyBy	1.229	0.005	1.235
plotVarPart-method	0.700	0.027	13.927
residuals-VarParFitList-method	3.322	0.339	12.117
sortCols-method	0.811	0.032	14.313
varPartConfInf	6.064	0.040	25.349