Package: variancePartition

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.8.1.tar.gz

StartedAt: 2018-04-12 10:38:24 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:42:59 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 275.3 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_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/variancePartition.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.1’
* 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         22.995  1.973  38.981
extractVarPart                 13.739  0.805  26.558
getVarianceComponents           4.616  0.502  17.924
varPartConfInf                  4.559  0.029  21.740
residuals-VarParFitList-method  3.141  0.382  16.743
fitExtractVarPartModel-method   1.651  0.089  21.847
plotCorrStructure               1.565  0.045   7.763
plotPercentBars                 1.345  0.033  11.859
plotVarPart-method              0.625  0.028  12.567
sortCols-method                 0.603  0.030  12.376
* 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	1.316	0.020	1.356
as.matrix-varPartResults-method	1.680	0.006	1.717
calcVarPart-method	0.147	0.003	0.150
canCorPairs	0.296	0.004	0.301
colinearityScore	0.602	0.004	0.611
extractVarPart	13.739	0.805	26.558
fitExtractVarPartModel-method	1.651	0.089	21.847
fitVarPartModel-method	22.995	1.973	38.981
getVarianceComponents	4.616	0.502	17.924
ggColorHue	0	0	0
plotCorrMatrix	0.683	0.004	0.704
plotCorrStructure	1.565	0.045	7.763
plotPercentBars	1.345	0.033	11.859
plotStratify	1.022	0.008	1.054
plotStratifyBy	0.829	0.004	0.851
plotVarPart-method	0.625	0.028	12.567
residuals-VarParFitList-method	3.141	0.382	16.743
sortCols-method	0.603	0.030	12.376
varPartConfInf	4.559	0.029	21.740