BioC 3.6: CHECK report for variancePartition on malbec1

Package: variancePartition

Version: 1.7.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.7.0.tar.gz

StartedAt: 2017-08-16 02:57:12 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:01:22 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 249.8 seconds

RetCode: 0

Status:  OK

CheckDir: variancePartition.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/variancePartition.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.0’
* 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 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         22.324  0.964  41.907
extractVarPart                 13.324  0.424  27.154
getVarianceComponents           4.908  0.576  14.583
varPartConfInf                  3.832  0.464  17.316
residuals-VarParFitList-method  3.172  0.608  13.367
fitExtractVarPartModel-method   1.432  0.252  19.960
plotCorrStructure               1.220  0.356   7.289
plotPercentBars                 1.064  0.408  11.749
sortCols-method                 0.640  0.356  11.027
plotVarPart-method              0.504  0.336  10.671
* 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	0.532	0.012	0.556
as.matrix-varPartResults-method	1.348	0.004	1.354
calcVarPart-method	0.124	0.000	0.121
canCorPairs	0.256	0.000	0.255
colinearityScore	0.808	0.000	0.810
extractVarPart	13.324	0.424	27.154
fitExtractVarPartModel-method	1.432	0.252	19.960
fitVarPartModel-method	22.324	0.964	41.907
getVarianceComponents	4.908	0.576	14.583
ggColorHue	0.004	0.000	0.001
plotCorrMatrix	0.472	0.000	0.471
plotCorrStructure	1.220	0.356	7.289
plotPercentBars	1.064	0.408	11.749
plotStratify	0.932	0.084	1.015
plotStratifyBy	0.720	0.020	0.738
plotVarPart-method	0.504	0.336	10.671
residuals-VarParFitList-method	3.172	0.608	13.367
sortCols-method	0.640	0.356	11.027
varPartConfInf	3.832	0.464	17.316