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BioC 3.2: CHECK report for RUVcorr on perceval

This page was generated on 2015-11-10 14:49:46 -0800 (Tue, 10 Nov 2015).

Package 931/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVcorr 1.2.0
Saskia Freytag
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/RUVcorr
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: RUVcorr
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RUVcorr_1.2.0.tar.gz
StartedAt: 2015-11-10 09:15:21 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 09:16:25 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 64.4 seconds
RetCode: 0
Status:  OK 
CheckDir: RUVcorr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RUVcorr_1.2.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RUVcorr.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RUVcorr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RUVcorr’ version ‘1.2.0’
* 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 ‘RUVcorr’ can be installed ... [3s/3s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [28s/28s] OK
* 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

RUVcorr.Rcheck/00install.out:

* installing *source* package ‘RUVcorr’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RUVcorr)

RUVcorr.Rcheck/RUVcorr-Ex.timings:

nameusersystemelapsed
ECDFPlot1.5540.0301.587
PCAPlot2.5700.0262.600
RLEPlot2.5970.0452.643
RUVNaiveRidge0.6770.0110.688
assessQuality0.2330.0090.242
background0.1440.0020.146
calculateThreshold2.8510.0702.921
compareRanks1.1630.0141.177
correlationPlot0.1470.0110.159
eigenvaluePlot0.3820.0120.393
empNegativeControls0.3630.0070.370
findWeights0.8610.0150.877
genePlot0.3480.0090.358
histogramPlot0.5310.0230.555
is.optimizeParameters0.0010.0000.001
is.simulateGEdata0.0000.0010.001
optimizeParameters2.3620.0362.399
plot.optimizeParameters3.2090.0633.273
plotDesign0.8710.0310.965
plotThreshold2.8460.0282.876
print.simulateGEdata000
prioritise0.9990.0321.031
simulateGEdata0.9570.0180.976
wcor0.9670.0230.990