Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2025-08-28 12:05 -0400 (Thu, 28 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4822
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4613
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4556
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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

Package 1423/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nearBynding 1.19.1  (landing page)
Veronica Busa
Snapshot Date: 2025-08-27 13:45 -0400 (Wed, 27 Aug 2025)
git_url: https://git.bioconductor.org/packages/nearBynding
git_branch: devel
git_last_commit: ab750a4
git_last_commit_date: 2025-07-23 13:23:21 -0400 (Wed, 23 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for nearBynding on lconway

To the developers/maintainers of the nearBynding package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: nearBynding
Version: 1.19.1
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_1.19.1.tar.gz
StartedAt: 2025-08-27 22:25:41 -0400 (Wed, 27 Aug 2025)
EndedAt: 2025-08-27 22:31:12 -0400 (Wed, 27 Aug 2025)
EllapsedTime: 330.7 seconds
RetCode: 0
Status:   OK  
CheckDir: nearBynding.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/nearBynding.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nearBynding/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nearBynding’ version ‘1.19.1’
* 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 ... INFO
  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 code 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           20.223  0.636  20.946
visualizeCapRStereogene   6.915  0.110   7.057
visualizeStereogene       6.304  0.067   6.417
GenomeMappingToChainFile  5.266  0.131   5.423
liftOverToExomicBG        4.989  0.039   5.052
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘nearBynding’ ...
** this is package ‘nearBynding’ version ‘1.19.1’
** 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
CleanBAMtoBG0.0370.0160.066
CleanBEDtoBG0.0140.0260.074
ExtractTranscriptomeSequence0.0000.0010.001
GenomeMappingToChainFile5.2660.1315.423
assessGrouping1.1030.0281.134
bindingContextDistance0.1610.0180.184
bindingContextDistanceCapR0.4080.0250.436
getChainChrSize4.1810.0334.234
get_outfiles0.0060.0160.022
liftOverToExomicBG4.9890.0395.052
nearBynding-package0.0010.0010.001
processCapRout20.223 0.63620.946
runCapR0.0040.0070.017
runStereogene0.0030.0060.016
runStereogeneOnCapR0.0190.0330.104
symmetryCapR0.3190.0200.341
symmetryContext0.0540.0140.068
visualizeCapRStereogene6.9150.1107.057
visualizeStereogene6.3040.0676.417
write_config0.0000.0000.001
write_fasta0.0000.0010.001