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CHECK report for BadRegionFinder on malbec1

This page was generated on 2018-04-12 13:14:50 -0400 (Thu, 12 Apr 2018).

Package 85/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BadRegionFinder 1.6.0
Sarah Sandmann
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BadRegionFinder
Branch: RELEASE_3_6
Last Commit: 6d7be50
Last Changed Date: 2017-10-30 12:41:15 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BadRegionFinder
Version: 1.6.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BadRegionFinder_1.6.0.tar.gz
StartedAt: 2018-04-11 21:36:02 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:39:20 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 197.9 seconds
RetCode: 0
Status:  OK 
CheckDir: BadRegionFinder.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BadRegionFinder_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BadRegionFinder.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BadRegionFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BadRegionFinder’ version ‘1.6.0’
* 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 ‘BadRegionFinder’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotDetailed     7.216  0.060  11.973
plotSummaryGenes 3.424  0.016   7.136
* 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

BadRegionFinder.Rcheck/00install.out

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

Tests output


Example timings

BadRegionFinder.Rcheck/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.2640.0040.269
determineCoverage0.0080.0000.004
determineCoverageQuality0.0040.0000.003
determineQuantiles0.5680.0080.575
determineRegionsOfInterest0.0000.0040.003
plotDetailed 7.216 0.06011.973
plotSummary0.1760.0000.178
plotSummaryGenes3.4240.0167.136
reportBadRegionsDetailed0.1560.0080.164
reportBadRegionsGenes0.1640.0000.165
reportBadRegionsSummary0.1720.0040.176