BioC 3.2: CHECK report for variancePartition on zin1

Package: variancePartition

Version: 0.99.6

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_0.99.6.tar.gz

StartedAt: 2015-08-24 04:33:09 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:35:44 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 154.6 seconds

RetCode: 0

Status:  OK

CheckDir: variancePartition.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_0.99.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/variancePartition.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘0.99.6’
* 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 ... [6s/6s] 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 ... [34s/92s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
fitVarPartModel-method         15.503  0.790  32.340
extractVarPart                  6.006  0.290  15.423
residuals-VarParFitList-method  3.277  0.462  10.566
fitExtractVarPartModel-method   1.430  0.264  13.924
plotVarPart                     0.620  0.280   7.329
sortCols                        0.544  0.276   7.576
* 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	0.081	0.000	0.081
colinearityScore	0.481	0.008	0.488
extractVarPart	6.006	0.290	15.423
fitExtractVarPartModel-method	1.430	0.264	13.924
fitVarPartModel-method	15.503	0.790	32.340
ggColorHue	0.000	0.000	0.001
plotStratifyBy	0.893	0.040	0.931
plotVarPart	0.620	0.280	7.329
residuals-VarParFitList-method	3.277	0.462	10.566
sortCols	0.544	0.276	7.576