BioC 3.4: CHECK report for variancePartition on zin1

Package: variancePartition

Version: 1.3.10

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.3.10.tar.gz

StartedAt: 2016-09-20 13:38:07 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:41:10 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 183.3 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_1.3.10.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/variancePartition.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.10’
* 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         18.432  0.728  31.406
extractVarPart                 10.064  0.312  17.900
varPartConfInf                  4.460  0.408  16.367
getVarianceComponents           3.444  0.452   8.656
residuals-VarParFitList-method  1.980  0.332   7.828
fitExtractVarPartModel-method   0.936  0.132  14.387
plotVarPart-method              0.652  0.256   7.196
plotPercentBars                 0.636  0.220   6.823
sortCols-method                 0.540  0.232   6.863
* 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	0.172	0.000	0.181
calcVarPart-method	0.072	0.000	0.073
canCorPairs	0.048	0.000	0.045
colinearityScore	0.560	0.004	0.564
extractVarPart	10.064	0.312	17.900
fitExtractVarPartModel-method	0.936	0.132	14.387
fitVarPartModel-method	18.432	0.728	31.406
getVarianceComponents	3.444	0.452	8.656
ggColorHue	0.004	0.000	0.001
plotCorrMatrix	0.072	0.000	0.074
plotCorrStructure	0.792	0.232	4.225
plotPercentBars	0.636	0.220	6.823
plotStratify	0.716	0.028	0.744
plotStratifyBy	0.708	0.036	0.744
plotVarPart-method	0.652	0.256	7.196
residuals-VarParFitList-method	1.980	0.332	7.828
sortCols-method	0.540	0.232	6.863
varPartConfInf	4.460	0.408	16.367