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This page was generated on 2021-11-24 15:05:14 -0500 (Wed, 24 Nov 2021).

CHECK results for RUVcorr on nebbiolo2

To the developers/maintainers of the RUVcorr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RUVcorr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1680/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVcorr 1.26.0  (landing page)
Saskia Freytag
Snapshot Date: 2021-11-23 04:15:06 -0500 (Tue, 23 Nov 2021)
git_url: https://git.bioconductor.org/packages/RUVcorr
git_branch: RELEASE_3_14
git_last_commit: 303fb49
git_last_commit_date: 2021-10-26 12:19:54 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RUVcorr
Version: 1.26.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings RUVcorr_1.26.0.tar.gz
StartedAt: 2021-11-23 10:51:22 -0500 (Tue, 23 Nov 2021)
EndedAt: 2021-11-23 10:52:01 -0500 (Tue, 23 Nov 2021)
EllapsedTime: 39.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RUVcorr.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings RUVcorr_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/RUVcorr.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.26.0’
* 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 ... WARNING
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘RUVcorr’
* 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: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/RUVcorr.Rcheck/00check.log’
for details.



Installation output

RUVcorr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL RUVcorr
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-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
ECDFPlot0.6180.0390.658
PCAPlot1.4920.0041.496
RLEPlot1.2700.0121.282
RUVNaiveRidge0.3890.0160.406
assessQuality0.0730.0000.073
background0.0590.0000.058
calculateThreshold1.1860.0001.187
compareRanks0.7850.0080.793
correlationPlot0.0970.0070.105
eigenvaluePlot0.2380.0170.254
empNegativeControls0.2690.1050.374
findWeights0.2780.0240.303
genePlot0.1450.0190.166
histogramPlot0.2630.0080.272
is.optimizeParameters000
is.simulateGEdata000
optimizeParameters1.2870.0041.291
plot.optimizeParameters1.5480.0031.552
plotDesign0.4090.0200.429
plotThreshold1.2410.0161.257
print.simulateGEdata000
prioritise0.2800.0200.301
simulateGEdata0.3160.0000.316
wcor0.3890.0000.389