BioC 3.5: CHECK report for variancePartition on toluca2

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: 2017-04-23 11:02:54 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 11:08:50 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 355.2 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 r72187)
* 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         24.021  1.701  50.239
extractVarPart                 14.666  0.654  35.435
varPartConfInf                  6.007  0.030  30.790
getVarianceComponents           4.786  0.937  19.744
residuals-VarParFitList-method  3.078  0.321  18.095
fitExtractVarPartModel-method   1.963  0.073  29.937
plotCorrStructure               1.796  0.066  10.927
plotPercentBars                 1.725  0.052  20.405
sortCols-method                 0.808  0.030  19.878
plotVarPart-method              0.793  0.026  18.638
* 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	0.829	0.013	0.844
as.matrix-varPartResults-method	2.082	0.024	2.107
calcVarPart-method	0.184	0.002	0.186
canCorPairs	0.366	0.004	0.371
colinearityScore	1.173	0.005	1.179
extractVarPart	14.666	0.654	35.435
fitExtractVarPartModel-method	1.963	0.073	29.937
fitVarPartModel-method	24.021	1.701	50.239
getVarianceComponents	4.786	0.937	19.744
ggColorHue	0.001	0.000	0.001
plotCorrMatrix	0.826	0.020	0.890
plotCorrStructure	1.796	0.066	10.927
plotPercentBars	1.725	0.052	20.405
plotStratify	1.384	0.009	1.435
plotStratifyBy	1.154	0.004	1.171
plotVarPart-method	0.793	0.026	18.638
residuals-VarParFitList-method	3.078	0.321	18.095
sortCols-method	0.808	0.030	19.878
varPartConfInf	6.007	0.030	30.790