BioC 3.4: CHECK report for variancePartition on malbec1

Package: variancePartition

Version: 1.4.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.4.2.tar.gz

StartedAt: 2017-04-15 01:46:47 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:50:35 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 228.9 seconds

RetCode: 0

Status:  OK

CheckDir: variancePartition.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.4.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/variancePartition.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.2’
* 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         22.556  0.820  37.946
extractVarPart                 11.628  0.320  23.430
varPartConfInf                  4.928  0.432  17.945
getVarianceComponents           4.480  0.632  11.244
residuals-VarParFitList-method  2.716  0.544   9.656
fitExtractVarPartModel-method   1.040  0.236  16.806
plotCorrStructure               0.804  0.336   5.379
plotPercentBars                 0.804  0.308   8.703
sortCols-method                 0.704  0.352   8.804
plotVarPart-method              0.580  0.344   8.131
* 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	0.192	0.008	0.215
as.matrix-varPartResults-method	0.452	0.000	0.452
calcVarPart-method	0.076	0.000	0.077
canCorPairs	0.052	0.000	0.053
colinearityScore	0.604	0.000	0.944
extractVarPart	11.628	0.320	23.430
fitExtractVarPartModel-method	1.040	0.236	16.806
fitVarPartModel-method	22.556	0.820	37.946
getVarianceComponents	4.480	0.632	11.244
ggColorHue	0	0	0
plotCorrMatrix	0.104	0.000	0.104
plotCorrStructure	0.804	0.336	5.379
plotPercentBars	0.804	0.308	8.703
plotStratify	0.952	0.036	0.988
plotStratifyBy	0.884	0.060	0.944
plotVarPart-method	0.580	0.344	8.131
residuals-VarParFitList-method	2.716	0.544	9.656
sortCols-method	0.704	0.352	8.804
varPartConfInf	4.928	0.432	17.945