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

EndedAt: 2017-08-16 09:13:47 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 318.4 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 3.4.1 (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 ‘1.6.0’
* 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         22.247  1.704  44.241
extractVarPart                 12.174  0.631  31.258
getVarianceComponents           4.810  0.825  24.183
varPartConfInf                  5.134  0.124  24.359
residuals-VarParFitList-method  3.074  0.322  23.393
plotCorrStructure               1.465  0.075   9.296
plotPercentBars                 1.419  0.066  17.042
fitExtractVarPartModel-method   1.311  0.075  26.220
plotVarPart-method              0.591  0.029  16.289
sortCols-method                 0.582  0.033  15.201
* 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	0.813	0.020	0.864
as.matrix-varPartResults-method	1.616	0.018	1.656
calcVarPart-method	0.138	0.002	0.144
canCorPairs	0.254	0.004	0.260
colinearityScore	0.884	0.003	0.893
extractVarPart	12.174	0.631	31.258
fitExtractVarPartModel-method	1.311	0.075	26.220
fitVarPartModel-method	22.247	1.704	44.241
getVarianceComponents	4.810	0.825	24.183
ggColorHue	0.001	0.000	0.000
plotCorrMatrix	0.553	0.020	0.603
plotCorrStructure	1.465	0.075	9.296
plotPercentBars	1.419	0.066	17.042
plotStratify	1.213	0.008	1.273
plotStratifyBy	0.977	0.004	1.004
plotVarPart-method	0.591	0.029	16.289
residuals-VarParFitList-method	3.074	0.322	23.393
sortCols-method	0.582	0.033	15.201
varPartConfInf	5.134	0.124	24.359