BioC 3.5: CHECK report for variancePartition on toluca2
This page was generated on 2017-04-23 14:40:21 -0400 (Sun, 23 Apr 2017).
variancePartition 1.5.7 Gabriel E. Hoffman
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/variancePartition | Last Changed Rev: 126598 / Revision: 129046 | Last Changed Date: 2017-02-08 11:16:41 -0500 (Wed, 08 Feb 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK |  |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK |  |
Summary
Package: variancePartition |
Version: 1.5.7 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.5.7.tar.gz |
StartedAt: 2017-04-23 11:02:54 -0400 (Sun, 23 Apr 2017) |
EndedAt: 2017-04-23 11:08:50 -0400 (Sun, 23 Apr 2017) |
EllapsedTime: 355.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: variancePartition.Rcheck |
Warnings: 0 |
Command output
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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_1.5.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/variancePartition.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.5.7’
* 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 ... 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 24.021 1.701 50.239
extractVarPart 14.666 0.654 35.435
varPartConfInf 6.007 0.030 30.790
getVarianceComponents 4.786 0.937 19.744
residuals-VarParFitList-method 3.078 0.321 18.095
fitExtractVarPartModel-method 1.963 0.073 29.937
plotCorrStructure 1.796 0.066 10.927
plotPercentBars 1.725 0.052 20.405
sortCols-method 0.808 0.030 19.878
plotVarPart-method 0.793 0.026 18.638
* 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:
name | user | system | elapsed
|
ESS-method | 0.829 | 0.013 | 0.844 |
|
as.matrix-varPartResults-method | 2.082 | 0.024 | 2.107 |
|
calcVarPart-method | 0.184 | 0.002 | 0.186 |
|
canCorPairs | 0.366 | 0.004 | 0.371 |
|
colinearityScore | 1.173 | 0.005 | 1.179 |
|
extractVarPart | 14.666 | 0.654 | 35.435 |
|
fitExtractVarPartModel-method | 1.963 | 0.073 | 29.937 |
|
fitVarPartModel-method | 24.021 | 1.701 | 50.239 |
|
getVarianceComponents | 4.786 | 0.937 | 19.744 |
|
ggColorHue | 0.001 | 0.000 | 0.001 |
|
plotCorrMatrix | 0.826 | 0.020 | 0.890 |
|
plotCorrStructure | 1.796 | 0.066 | 10.927 |
|
plotPercentBars | 1.725 | 0.052 | 20.405 |
|
plotStratify | 1.384 | 0.009 | 1.435 |
|
plotStratifyBy | 1.154 | 0.004 | 1.171 |
|
plotVarPart-method | 0.793 | 0.026 | 18.638 |
|
residuals-VarParFitList-method | 3.078 | 0.321 | 18.095 |
|
sortCols-method | 0.808 | 0.030 | 19.878 |
|
varPartConfInf | 6.007 | 0.030 | 30.790 |
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