BioC 3.4: CHECK report for variancePartition on morelia

Package: variancePartition

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.4.2.tar.gz

StartedAt: 2017-04-15 09:09:08 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 09:13:24 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 256.1 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_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/variancePartition.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.2’
* 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 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         21.588  1.392  36.224
extractVarPart                 12.479  0.658  23.117
varPartConfInf                  6.112  0.037  26.365
getVarianceComponents           4.159  0.452  11.154
residuals-VarParFitList-method  2.824  0.295   9.723
fitExtractVarPartModel-method   1.177  0.086  22.889
plotCorrStructure               1.067  0.037   6.569
plotVarPart-method              0.847  0.034  12.244
plotPercentBars                 0.848  0.028  10.869
sortCols-method                 0.780  0.042  12.213
* 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	0.213	0.006	0.267
as.matrix-varPartResults-method	0.431	0.003	0.435
calcVarPart-method	0.084	0.001	0.086
canCorPairs	0.059	0.003	0.062
colinearityScore	0.489	0.004	0.492
extractVarPart	12.479	0.658	23.117
fitExtractVarPartModel-method	1.177	0.086	22.889
fitVarPartModel-method	21.588	1.392	36.224
getVarianceComponents	4.159	0.452	11.154
ggColorHue	0.001	0.000	0.000
plotCorrMatrix	0.102	0.004	0.107
plotCorrStructure	1.067	0.037	6.569
plotPercentBars	0.848	0.028	10.869
plotStratify	1.060	0.003	1.064
plotStratifyBy	1.338	0.008	1.348
plotVarPart-method	0.847	0.034	12.244
residuals-VarParFitList-method	2.824	0.295	9.723
sortCols-method	0.780	0.042	12.213
varPartConfInf	6.112	0.037	26.365