BioC 3.2: CHECK report for variancePartition on oaxaca

Package: variancePartition

Version: 1.0.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.0.7.tar.gz

StartedAt: 2016-04-23 05:11:13 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:15:24 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 250.4 seconds

RetCode: 0

Status:  OK

CheckDir: variancePartition.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.0.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/variancePartition.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.7’
* 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 ... [9s/9s] 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 ... [59s/163s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
fitVarPartModel-method         24.082  1.428  42.233
extractVarPart                 14.343  0.666  27.889
getVarianceComponents           4.353  0.425  12.128
residuals-VarParFitList-method  3.116  0.303  11.131
fitExtractVarPartModel-method   1.385  0.086  27.077
plotPercentBars                 0.888  0.028  12.368
plotVarPart-method              0.788  0.037  12.258
sortCols-method                 0.770  0.037  12.108
* 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
calcVarPart-method	0.221	0.006	0.316
colinearityScore	0.646	0.005	0.650
extractVarPart	14.343	0.666	27.889
fitExtractVarPartModel-method	1.385	0.086	27.077
fitVarPartModel-method	24.082	1.428	42.233
getVarianceComponents	4.353	0.425	12.128
ggColorHue	0.000	0.000	0.001
plotPercentBars	0.888	0.028	12.368
plotStratifyBy	0.856	0.004	0.864
plotVarPart-method	0.788	0.037	12.258
residuals-VarParFitList-method	3.116	0.303	11.131
sortCols-method	0.770	0.037	12.108