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This page was generated on 2023-04-12 11:06:17 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 nearBynding on lconway


To the developers/maintainers of the nearBynding package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nearBynding.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 1334/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nearBynding 1.8.0  (landing page)
Veronica Busa
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/nearBynding
git_branch: RELEASE_3_16
git_last_commit: 5cd681f
git_last_commit_date: 2022-11-01 11:22:51 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: nearBynding
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nearBynding.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nearBynding_1.8.0.tar.gz
StartedAt: 2023-04-10 21:30:58 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:35:21 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 262.4 seconds
RetCode: 0
Status:   OK  
CheckDir: nearBynding.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nearBynding.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nearBynding_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/nearBynding.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.8.0’
* 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  7.1Mb
  sub-directories of 1Mb or more:
    extdata   6.9Mb
* 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          15.761  0.688  16.525
visualizeCapRStereogene  5.707  0.104   5.834
* 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-3.16-bioc/meat/nearBynding.Rcheck/00check.log’
for details.



Installation output

nearBynding.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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
CleanBAMtoBG0.0340.0150.076
CleanBEDtoBG0.0150.0260.089
ExtractTranscriptomeSequence0.0000.0000.001
GenomeMappingToChainFile3.4510.0573.517
assessGrouping1.0740.0401.116
bindingContextDistance0.1420.0120.160
bindingContextDistanceCapR0.3560.0280.386
getChainChrSize4.0250.0314.062
get_outfiles0.0030.0120.017
liftOverToExomicBG3.9050.0223.934
nearBynding-package0.0000.0010.001
processCapRout15.761 0.68816.525
runCapR0.0040.0080.026
runStereogene0.0030.0060.019
runStereogeneOnCapR0.0180.0330.098
symmetryCapR0.3610.0210.388
symmetryContext0.0660.0190.093
visualizeCapRStereogene5.7070.1045.834
visualizeStereogene4.7810.0394.831
write_config000
write_fasta0.0000.0000.001