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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 2024/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SOMNiBUS 1.17.0  (landing page)
Kathleen Klein
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/SOMNiBUS
git_branch: devel
git_last_commit: 83171d7
git_last_commit_date: 2025-04-15 12:18:18 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SOMNiBUS on lconway

To the developers/maintainers of the SOMNiBUS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SOMNiBUS.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: SOMNiBUS
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SOMNiBUS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SOMNiBUS_1.17.0.tar.gz
StartedAt: 2025-08-09 00:12:38 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 00:28:32 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 953.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SOMNiBUS.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SOMNiBUS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SOMNiBUS_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SOMNiBUS.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 ‘SOMNiBUS/DESCRIPTION’ ... OK
* this is package ‘SOMNiBUS’ version ‘1.17.0’
* 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 ‘SOMNiBUS’ 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 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 whether startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
binomRegMethModel     217.281 17.191 235.922
runSOMNiBUS           179.750 19.127 200.454
binomRegMethPredPlot   27.484  5.289  33.119
binomRegMethModelPlot  27.383  5.190  32.928
binomRegMethModelPred  26.172  5.135  31.628
splitDataByGene        18.940  1.799  20.930
splitDataByChromatin   10.306  0.550  11.118
formatFromBismark       4.698  0.413   5.132
* 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

SOMNiBUS.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SOMNiBUS’ ...
** this is package ‘SOMNiBUS’ version ‘1.17.0’
** using staged installation
** R
** data
** 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 (SOMNiBUS)

Tests output


Example timings

SOMNiBUS.Rcheck/SOMNiBUS-Ex.timings

nameusersystemelapsed
binomRegMethModel217.281 17.191235.922
binomRegMethModelPlot27.383 5.19032.928
binomRegMethModelPred26.172 5.13531.628
binomRegMethModelSim1.5280.2821.827
binomRegMethPredPlot27.484 5.28933.119
formatFromBSseq0.1380.0030.143
formatFromBismark4.6980.4135.132
runSOMNiBUS179.750 19.127200.454
splitDataByChromatin10.306 0.55011.118
splitDataByDensity2.5820.0672.661
splitDataByGRanges0.2340.0130.250
splitDataByGene18.940 1.79920.930
splitDataByRegion0.0150.0120.027