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This page was generated on 2022-08-12 13:20:34 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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 nebbiolo1


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 1309/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nearBynding 1.6.0  (landing page)
Veronica Busa
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/nearBynding
git_branch: RELEASE_3_15
git_last_commit: 951bb7c
git_last_commit_date: 2022-04-26 12:08:28 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: nearBynding
Version: 1.6.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:nearBynding.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings nearBynding_1.6.0.tar.gz
StartedAt: 2022-08-11 21:12:01 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 21:16:33 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 271.4 seconds
RetCode: 0
Status:   OK  
CheckDir: nearBynding.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:nearBynding.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings nearBynding_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/nearBynding.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’
* 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 ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
processCapRout          16.754  0.412  17.168
visualizeCapRStereogene  5.663  0.024   5.686
* 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: OK


Installation output

nearBynding.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL nearBynding
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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
CleanBAMtoBG0.0350.0020.037
CleanBEDtoBG0.0110.0040.014
ExtractTranscriptomeSequence000
GenomeMappingToChainFile3.7630.0203.785
assessGrouping2.5080.0042.512
bindingContextDistance0.2650.0080.280
bindingContextDistanceCapR0.4990.0160.514
getChainChrSize4.4680.0844.552
get_outfiles0.0030.0040.006
liftOverToExomicBG3.9450.0764.021
nearBynding-package0.0010.0000.001
processCapRout16.754 0.41217.168
runCapR0.0020.0000.003
runStereogene0.0010.0010.002
runStereogeneOnCapR0.0090.0010.009
symmetryCapR0.4990.0080.507
symmetryContext0.0760.0040.079
visualizeCapRStereogene5.6630.0245.686
visualizeStereogene4.810.024.83
write_config0.0010.0000.001
write_fasta0.0000.0010.001