BioC 3.5: CHECK report for variancePartition on veracruz2

Package: variancePartition

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.6.0.tar.gz

StartedAt: 2017-10-18 10:00:37 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 10:05:26 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 288.8 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/variancePartition.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.0’
* 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 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         23.114  1.873  39.476
extractVarPart                 12.779  0.719  26.480
getVarianceComponents           4.791  0.880  21.286
varPartConfInf                  5.185  0.051  24.758
residuals-VarParFitList-method  3.010  0.360  17.623
fitExtractVarPartModel-method   1.487  0.075  22.604
plotCorrStructure               1.329  0.074   7.768
plotPercentBars                 1.274  0.064  12.822
sortCols-method                 0.667  0.030  13.312
plotVarPart-method              0.534  0.026  11.716
* 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	0.774	0.020	0.822
as.matrix-varPartResults-method	1.678	0.030	1.838
calcVarPart-method	0.145	0.003	0.151
canCorPairs	0.295	0.007	0.307
colinearityScore	0.618	0.008	0.636
extractVarPart	12.779	0.719	26.480
fitExtractVarPartModel-method	1.487	0.075	22.604
fitVarPartModel-method	23.114	1.873	39.476
getVarianceComponents	4.791	0.880	21.286
ggColorHue	0.000	0.000	0.001
plotCorrMatrix	0.603	0.024	0.660
plotCorrStructure	1.329	0.074	7.768
plotPercentBars	1.274	0.064	12.822
plotStratify	1.133	0.011	1.192
plotStratifyBy	0.791	0.006	0.814
plotVarPart-method	0.534	0.026	11.716
residuals-VarParFitList-method	3.010	0.360	17.623
sortCols-method	0.667	0.030	13.312
varPartConfInf	5.185	0.051	24.758