Package: variancePartition

Version: 1.8.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.8.1.tar.gz

StartedAt: 2018-04-12 03:31:13 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:34:59 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 225.4 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_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/variancePartition.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.1’
* 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 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         21.900  1.084  38.075
extractVarPart                 13.372  0.420  22.962
getVarianceComponents           4.624  0.740  11.623
varPartConfInf                  4.228  0.536  18.030
residuals-VarParFitList-method  3.288  0.612  10.885
fitExtractVarPartModel-method   1.748  0.292  17.079
plotCorrStructure               1.236  0.436   6.402
plotPercentBars                 1.120  0.368   9.191
sortCols-method                 0.692  0.336  10.327
plotVarPart-method              0.568  0.356   8.946
* 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	0.976	0.004	0.982
as.matrix-varPartResults-method	1.340	0.000	1.341
calcVarPart-method	0.124	0.000	0.121
canCorPairs	0.236	0.008	0.243
colinearityScore	0.492	0.000	0.496
extractVarPart	13.372	0.420	22.962
fitExtractVarPartModel-method	1.748	0.292	17.079
fitVarPartModel-method	21.900	1.084	38.075
getVarianceComponents	4.624	0.740	11.623
ggColorHue	0.000	0.000	0.001
plotCorrMatrix	0.488	0.012	0.501
plotCorrStructure	1.236	0.436	6.402
plotPercentBars	1.120	0.368	9.191
plotStratify	0.988	0.112	1.099
plotStratifyBy	0.744	0.032	0.779
plotVarPart-method	0.568	0.356	8.946
residuals-VarParFitList-method	3.288	0.612	10.885
sortCols-method	0.692	0.336	10.327
varPartConfInf	4.228	0.536	18.030