BioC 3.5: CHECK report for variancePartition on malbec2

Package: variancePartition

Version: 1.6.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.6.0.tar.gz

StartedAt: 2017-10-18 03:04:02 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:07:57 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 235.8 seconds

RetCode: 0

Status:  OK

CheckDir: variancePartition.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/variancePartition.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 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         21.772  0.912  37.236
extractVarPart                 13.148  0.428  23.916
getVarianceComponents           4.564  0.660  13.164
varPartConfInf                  4.180  0.548  18.760
residuals-VarParFitList-method  3.196  0.560  11.514
fitExtractVarPartModel-method   1.460  0.244  16.918
plotCorrStructure               1.196  0.356   6.989
plotPercentBars                 1.128  0.396  10.090
sortCols-method                 0.804  0.420  10.575
plotVarPart-method              0.536  0.332   9.843
* 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	0.736	0.008	0.977
as.matrix-varPartResults-method	1.248	0.004	1.254
calcVarPart-method	0.116	0.000	0.117
canCorPairs	0.248	0.004	0.253
colinearityScore	0.508	0.000	0.512
extractVarPart	13.148	0.428	23.916
fitExtractVarPartModel-method	1.460	0.244	16.918
fitVarPartModel-method	21.772	0.912	37.236
getVarianceComponents	4.564	0.660	13.164
ggColorHue	0	0	0
plotCorrMatrix	0.512	0.000	0.514
plotCorrStructure	1.196	0.356	6.989
plotPercentBars	1.128	0.396	10.090
plotStratify	1.008	0.124	1.136
plotStratifyBy	0.716	0.036	0.755
plotVarPart-method	0.536	0.332	9.843
residuals-VarParFitList-method	3.196	0.560	11.514
sortCols-method	0.804	0.420	10.575
varPartConfInf	4.180	0.548	18.760