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This page was generated on 2022-12-02 11:08:53 -0500 (Fri, 02 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4210
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4122
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4188
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for BadRegionFinder on merida1


To the developers/maintainers of the BadRegionFinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BadRegionFinder.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 104/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BadRegionFinder 1.27.0  (landing page)
Sarah Sandmann
Snapshot Date: 2022-12-01 14:00:17 -0500 (Thu, 01 Dec 2022)
git_url: https://git.bioconductor.org/packages/BadRegionFinder
git_branch: master
git_last_commit: 1b861d0
git_last_commit_date: 2022-11-01 11:13:25 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'VariantAnnotation' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'VariantAnnotation' which is not available

Summary

Package: BadRegionFinder
Version: 1.27.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BadRegionFinder_1.27.0.tar.gz
StartedAt: 2022-12-01 23:21:34 -0500 (Thu, 01 Dec 2022)
EndedAt: 2022-12-01 23:32:18 -0500 (Thu, 01 Dec 2022)
EllapsedTime: 643.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BadRegionFinder.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BadRegionFinder_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/BadRegionFinder.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* 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 ‘1.27.0’
* 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     21.077  0.674  30.199
plotSummaryGenes  5.796  0.063   8.751
* 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-3.17-bioc/meat/BadRegionFinder.Rcheck/00check.log’
for details.



Installation output

BadRegionFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BadRegionFinder
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/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-package0.3800.0260.549
determineCoverage0.0060.0020.008
determineCoverageQuality0.0050.0010.014
determineQuantiles0.3440.0290.496
determineRegionsOfInterest0.0050.0020.009
plotDetailed21.077 0.67430.199
plotSummary0.3290.0170.466
plotSummaryGenes5.7960.0638.751
reportBadRegionsDetailed0.3450.0170.499
reportBadRegionsGenes0.3460.0160.501
reportBadRegionsSummary0.3350.0170.490