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BioC 3.2: CHECK report for RUVcorr on zin1

This page was generated on 2015-08-24 10:50:32 -0700 (Mon, 24 Aug 2015).

Package 903/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVcorr 1.0.1
Saskia Freytag
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RUVcorr
Last Changed Rev: 104458 / Revision: 107696
Last Changed Date: 2015-06-01 20:10:17 -0700 (Mon, 01 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]NO, built version is LOWER than in internal repository!!!
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!

Summary

Package: RUVcorr
Version: 1.0.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RUVcorr_1.0.1.tar.gz
StartedAt: 2015-08-24 03:32:54 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 03:33:35 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 41.4 seconds
RetCode: 0
Status:  OK 
CheckDir: RUVcorr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RUVcorr_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RUVcorr.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 ‘RUVcorr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RUVcorr’ version ‘1.0.1’
* 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 ... [2s/2s] 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 ... [17s/17s] 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
ECDFPlot0.8770.0150.894
PCAPlot1.8150.0001.814
RLEPlot2.2820.0122.324
RUVNaiveRidge0.5530.0000.556
assessQuality0.0860.0000.090
background0.1160.0000.115
calculateThreshold1.4440.0001.444
compareRanks0.7930.0000.792
correlationPlot0.1180.0040.122
eigenvaluePlot0.2520.0000.252
empNegativeControls0.2440.0000.244
findWeights0.3060.0000.306
genePlot0.2780.0000.288
histogramPlot0.3470.0000.357
is.optimizeParameters000
is.simulateGEdata0.0000.0000.001
optimizeParameters1.6180.0041.623
plot.optimizeParameters1.8060.0041.812
plotDesign0.6260.0160.675
plotThreshold1.4800.0041.487
print.simulateGEdata0.0000.0000.001
prioritise0.3830.0080.390
simulateGEdata0.3680.0040.372
wcor0.3540.0000.354