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CHECK report for nearBynding on merida1

This page was generated on 2021-05-06 12:35:56 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the nearBynding package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1209/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nearBynding 1.0.0  (landing page)
Veronica Busa
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/nearBynding
Branch: RELEASE_3_12
Last Commit: ccf44ab
Last Changed Date: 2020-10-27 12:01:04 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: nearBynding
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nearBynding.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nearBynding_1.0.0.tar.gz
StartedAt: 2021-05-06 04:11:41 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:17:54 -0400 (Thu, 06 May 2021)
EllapsedTime: 373.4 seconds
RetCode: 0
Status:   OK  
CheckDir: nearBynding.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nearBynding.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nearBynding_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/nearBynding.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nearBynding/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nearBynding’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘nearBynding’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    extdata   8.1Mb
* 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 ... 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 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
processCapRout           24.679  0.550  25.339
visualizeCapRStereogene   8.938  0.086   9.049
visualizeStereogene       8.275  0.062   8.348
liftOverToExomicBG        6.546  0.039   6.592
GenomeMappingToChainFile  5.819  0.088   5.914
getChainChrSize           5.861  0.027   5.896
* 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/nearBynding.Rcheck/00check.log’
for details.



Installation output

nearBynding.Rcheck/00install.out

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

Tests output


Example timings

nearBynding.Rcheck/nearBynding-Ex.timings

nameusersystemelapsed
CleanBAMtoBG0.0400.0100.051
CleanBEDtoBG0.0130.0170.031
ExtractTranscriptomeSequence0.0000.0000.001
GenomeMappingToChainFile5.8190.0885.914
assessGrouping1.7670.0571.825
bindingContextDistance0.3110.0310.349
bindingContextDistanceCapR0.7350.0370.773
getChainChrSize5.8610.0275.896
get_outfiles0.0060.0220.029
liftOverToExomicBG6.5460.0396.592
nearBynding-package0.0010.0010.002
processCapRout24.679 0.55025.339
runCapR0.0040.0050.008
runStereogene0.0030.0040.007
runStereogeneOnCapR0.0170.0220.040
visualizeCapRStereogene8.9380.0869.049
visualizeStereogene8.2750.0628.348
write_config0.0000.0000.001
write_fasta0.0010.0000.001