BioC 3.6: CHECK report for variancePartition on veracruz1

Package: variancePartition

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.7.0.tar.gz

StartedAt: 2017-08-16 09:24:36 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 09:29:54 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 318.3 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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/variancePartition.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.0’
* 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         23.982  1.707  48.996
extractVarPart                 11.792  0.625  30.087
getVarianceComponents           4.816  0.903  24.151
varPartConfInf                  4.932  0.060  24.248
residuals-VarParFitList-method  3.046  0.319  22.237
fitExtractVarPartModel-method   1.404  0.073  25.638
plotCorrStructure               1.292  0.071   8.753
plotPercentBars                 1.206  0.063  16.889
sortCols-method                 0.674  0.032  15.679
plotVarPart-method              0.543  0.027  16.306
* 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	0.782	0.016	0.811
as.matrix-varPartResults-method	1.618	0.021	1.671
calcVarPart-method	0.122	0.002	0.126
canCorPairs	0.277	0.004	0.283
colinearityScore	0.905	0.005	0.921
extractVarPart	11.792	0.625	30.087
fitExtractVarPartModel-method	1.404	0.073	25.638
fitVarPartModel-method	23.982	1.707	48.996
getVarianceComponents	4.816	0.903	24.151
ggColorHue	0.001	0.000	0.000
plotCorrMatrix	0.637	0.020	0.667
plotCorrStructure	1.292	0.071	8.753
plotPercentBars	1.206	0.063	16.889
plotStratify	1.180	0.008	1.237
plotStratifyBy	1.019	0.004	1.060
plotVarPart-method	0.543	0.027	16.306
residuals-VarParFitList-method	3.046	0.319	22.237
sortCols-method	0.674	0.032	15.679
varPartConfInf	4.932	0.060	24.248