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CHECK report for RUVcorr on malbec2

This page was generated on 2020-10-17 11:55:39 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RUVcorr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1559/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVcorr 1.20.0
Saskia Freytag
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RUVcorr
Branch: RELEASE_3_11
Last Commit: bb5546f
Last Changed Date: 2020-04-27 14:48:10 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RUVcorr
Version: 1.20.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RUVcorr_1.20.0.tar.gz
StartedAt: 2020-10-17 05:06:08 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:06:54 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 46.5 seconds
RetCode: 0
Status:  OK 
CheckDir: RUVcorr.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RUVcorr_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/RUVcorr.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.20.0’
* 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 ... 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 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 files in ‘vignettes’ ... OK
* checking examples ... 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


Installation output

RUVcorr.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL RUVcorr
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘RUVcorr’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RUVcorr)

Tests output


Example timings

RUVcorr.Rcheck/RUVcorr-Ex.timings

nameusersystemelapsed
ECDFPlot0.6140.0120.626
PCAPlot1.4010.0041.405
RLEPlot1.6170.0121.629
RUVNaiveRidge0.3910.0080.399
assessQuality0.0640.0040.067
background0.0590.0000.059
calculateThreshold1.1210.0041.125
compareRanks0.7840.0000.785
correlationPlot0.1060.0040.109
eigenvaluePlot0.2250.0000.225
empNegativeControls0.1570.0040.160
findWeights0.2760.0000.275
genePlot0.180.000.18
histogramPlot0.2470.0000.247
is.optimizeParameters0.0000.0000.001
is.simulateGEdata000
optimizeParameters1.4120.0021.414
plot.optimizeParameters1.7500.0051.763
plotDesign0.6880.0080.720
plotThreshold1.3210.0001.321
print.simulateGEdata000
prioritise0.3920.0000.391
simulateGEdata0.3120.0080.320
wcor0.3850.0000.385