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BioC 3.5: CHECK report for variancePartition on veracruz2

This page was generated on 2017-10-18 14:33:31 -0400 (Wed, 18 Oct 2017).

Package 1354/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.6.0
Gabriel E. Hoffman
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/variancePartition
Branch: RELEASE_3_5
Last Commit: 163bf67
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  ERROR  OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: variancePartition
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.6.0.tar.gz
StartedAt: 2017-10-18 10:00:37 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 10:05:26 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 288.8 seconds
RetCode: 0
Status:  OK 
CheckDir: variancePartition.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/variancePartition.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.0’
* 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         23.114  1.873  39.476
extractVarPart                 12.779  0.719  26.480
getVarianceComponents           4.791  0.880  21.286
varPartConfInf                  5.185  0.051  24.758
residuals-VarParFitList-method  3.010  0.360  17.623
fitExtractVarPartModel-method   1.487  0.075  22.604
plotCorrStructure               1.329  0.074   7.768
plotPercentBars                 1.274  0.064  12.822
sortCols-method                 0.667  0.030  13.312
plotVarPart-method              0.534  0.026  11.716
* 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

variancePartition.Rcheck/00install.out:

* 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)

variancePartition.Rcheck/variancePartition-Ex.timings:

nameusersystemelapsed
ESS-method0.7740.0200.822
as.matrix-varPartResults-method1.6780.0301.838
calcVarPart-method0.1450.0030.151
canCorPairs0.2950.0070.307
colinearityScore0.6180.0080.636
extractVarPart12.779 0.71926.480
fitExtractVarPartModel-method 1.487 0.07522.604
fitVarPartModel-method23.114 1.87339.476
getVarianceComponents 4.791 0.88021.286
ggColorHue0.0000.0000.001
plotCorrMatrix0.6030.0240.660
plotCorrStructure1.3290.0747.768
plotPercentBars 1.274 0.06412.822
plotStratify1.1330.0111.192
plotStratifyBy0.7910.0060.814
plotVarPart-method 0.534 0.02611.716
residuals-VarParFitList-method 3.010 0.36017.623
sortCols-method 0.667 0.03013.312
varPartConfInf 5.185 0.05124.758