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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1401/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nearBynding 1.16.0  (landing page)
Veronica Busa
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/nearBynding
git_branch: RELEASE_3_20
git_last_commit: ca5a7c0
git_last_commit_date: 2024-10-29 10:50:26 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for nearBynding on merida1

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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2024-12-20 06:51:00 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 07:00:45 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 584.8 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/nearBynding.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.16.0’
* 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 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           35.766  0.934  37.309
visualizeCapRStereogene  13.521  0.163  14.101
visualizeStereogene      12.222  0.098  12.651
GenomeMappingToChainFile  9.643  0.338  10.322
liftOverToExomicBG        9.777  0.069   9.962
getChainChrSize           8.494  0.062   8.808
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/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
CleanBAMtoBG0.0560.0200.084
CleanBEDtoBG0.0210.0330.060
ExtractTranscriptomeSequence000
GenomeMappingToChainFile 9.643 0.33810.322
assessGrouping2.9180.0612.995
bindingContextDistance0.2400.0280.271
bindingContextDistanceCapR0.5850.0450.631
getChainChrSize8.4940.0628.808
get_outfiles0.0100.0260.040
liftOverToExomicBG9.7770.0699.962
nearBynding-package0.0000.0010.002
processCapRout35.766 0.93437.309
runCapR0.0040.0100.018
runStereogene0.0050.0080.015
runStereogeneOnCapR0.0280.0470.082
symmetryCapR0.6490.0490.701
symmetryContext0.0920.0270.120
visualizeCapRStereogene13.521 0.16314.101
visualizeStereogene12.222 0.09812.651
write_config0.0010.0000.001
write_fasta0.0010.0010.003