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CHECK report for BadRegionFinder on malbec1

This page was generated on 2020-09-21 11:01:16 -0400 (Mon, 21 Sep 2020).

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 104/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BadRegionFinder 1.17.0
Sarah Sandmann
Snapshot Date: 2020-09-20 14:41:51 -0400 (Sun, 20 Sep 2020)
URL: https://git.bioconductor.org/packages/BadRegionFinder
Branch: master
Last Commit: 5297ff3
Last Changed Date: 2020-04-27 14:56:28 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 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
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BadRegionFinder
Version: 1.17.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BadRegionFinder_1.17.0.tar.gz
StartedAt: 2020-09-21 03:00:43 -0400 (Mon, 21 Sep 2020)
EndedAt: 2020-09-21 03:05:41 -0400 (Mon, 21 Sep 2020)
EllapsedTime: 297.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BadRegionFinder.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BadRegionFinder_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BadRegionFinder.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.17.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotDetailed     10.524   0.20  12.557
plotSummaryGenes  4.680   0.02   6.436
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BadRegionFinder.Rcheck/00check.log’
for details.



Installation output

BadRegionFinder.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BadRegionFinder
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-package0.3080.0120.318
determineCoverage0.0040.0000.021
determineCoverageQuality0.0040.0000.004
determineQuantiles0.240.020.26
determineRegionsOfInterest0.0040.0000.003
plotDetailed10.524 0.20012.557
plotSummary0.2040.0040.212
plotSummaryGenes4.6800.0206.436
reportBadRegionsDetailed0.2720.0000.274
reportBadRegionsGenes0.2760.0000.278
reportBadRegionsSummary0.2280.0000.230