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CHECK report for BadRegionFinder on merida1

This page was generated on 2021-01-22 11:57:44 -0500 (Fri, 22 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE BadRegionFinder PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 109/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BadRegionFinder 1.18.0
Sarah Sandmann
Snapshot Date: 2021-01-21 14:42:12 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/BadRegionFinder
Branch: RELEASE_3_12
Last Commit: 54deba4
Last Changed Date: 2020-10-27 11:13:27 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BadRegionFinder
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BadRegionFinder_1.18.0.tar.gz
StartedAt: 2021-01-21 23:13:48 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 23:22:07 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 498.3 seconds
RetCode: 0
Status:  OK 
CheckDir: BadRegionFinder.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BadRegionFinder_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BadRegionFinder.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.18.0’
* 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 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 ... NOTE
determineCoverage: no visible global function definition for ‘path’
Undefined global functions or variables:
  path
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotDetailed     10.555  0.349  12.870
plotSummaryGenes  4.705  0.075   6.511
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/BadRegionFinder.Rcheck/00check.log’
for details.



Installation output

BadRegionFinder.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BadRegionFinder
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BadRegionFinder’ ...
** 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 (BadRegionFinder)

Tests output


Example timings

BadRegionFinder.Rcheck/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.2750.0190.297
determineCoverage0.0070.0020.009
determineCoverageQuality0.0040.0010.006
determineQuantiles0.2140.0210.237
determineRegionsOfInterest0.0040.0020.005
plotDetailed10.555 0.34912.870
plotSummary0.2190.0140.234
plotSummaryGenes4.7050.0756.511
reportBadRegionsDetailed0.2010.0120.214
reportBadRegionsGenes0.1790.0110.191
reportBadRegionsSummary0.2150.0130.228