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CHECK report for BadRegionFinder on malbec2

This page was generated on 2018-10-17 08:28:48 -0400 (Wed, 17 Oct 2018).

Package 87/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BadRegionFinder 1.8.0
Sarah Sandmann
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BadRegionFinder
Branch: RELEASE_3_7
Last Commit: c66c1a7
Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BadRegionFinder
Version: 1.8.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BadRegionFinder_1.8.0.tar.gz
StartedAt: 2018-10-15 22:35:23 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 22:38:23 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 179.2 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-3.7-bioc/R/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BadRegionFinder_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/BadRegionFinder.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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 or elapsed time > 5s
                  user system elapsed
plotDetailed     6.688  0.116  10.326
plotSummaryGenes 2.036  0.012   5.918
* 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-3.7-bioc/meat/BadRegionFinder.Rcheck/00check.log’
for details.



Installation output

BadRegionFinder.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL BadRegionFinder
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘BadRegionFinder’ ...
** 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
* DONE (BadRegionFinder)

Tests output


Example timings

BadRegionFinder.Rcheck/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.1600.0160.178
determineCoverage0.0040.0040.027
determineCoverageQuality0.0080.0000.006
determineQuantiles0.1960.0160.214
determineRegionsOfInterest0.0040.0000.004
plotDetailed 6.688 0.11610.326
plotSummary0.1560.0000.155
plotSummaryGenes2.0360.0125.918
reportBadRegionsDetailed0.1520.0040.159
reportBadRegionsGenes0.1400.0000.141
reportBadRegionsSummary0.1360.0080.144