BioC 3.3: CHECK report for variancePartition on zin2

Package: variancePartition

Version: 1.2.11

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.2.11.tar.gz

StartedAt: 2016-10-13 07:39:52 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:43:25 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 212.9 seconds

RetCode: 0

Status:  OK

CheckDir: variancePartition.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.2.11.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.2.11’
* 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         20.153  0.671  37.606
extractVarPart                 10.816  0.264  19.610
varPartConfInf                  5.064  0.400  17.485
getVarianceComponents           3.789  0.517  10.476
residuals-VarParFitList-method  2.217  0.409   9.253
plotCorrStructure               0.895  0.248   5.072
fitExtractVarPartModel-method   0.936  0.160  17.405
plotVarPart-method              0.697  0.277   8.114
plotPercentBars                 0.686  0.258   8.601
sortCols-method                 0.597  0.275   8.434
* 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	0.191	0.004	0.206
calcVarPart-method	0.086	0.000	0.085
canCorPairs	0.051	0.000	0.052
colinearityScore	0.660	0.004	0.666
extractVarPart	10.816	0.264	19.610
fitExtractVarPartModel-method	0.936	0.160	17.405
fitVarPartModel-method	20.153	0.671	37.606
getVarianceComponents	3.789	0.517	10.476
ggColorHue	0.001	0.000	0.000
plotCorrMatrix	0.087	0.000	0.088
plotCorrStructure	0.895	0.248	5.072
plotPercentBars	0.686	0.258	8.601
plotStratify	0.804	0.060	0.866
plotStratifyBy	0.723	0.040	0.768
plotVarPart-method	0.697	0.277	8.114
residuals-VarParFitList-method	2.217	0.409	9.253
sortCols-method	0.597	0.275	8.434
varPartConfInf	5.064	0.400	17.485