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This page was generated on 2024-12-23 12:08 -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 2004/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SOMNiBUS 1.14.2  (landing page)
Kathleen Klein
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/SOMNiBUS
git_branch: RELEASE_3_20
git_last_commit: 00bc0e3
git_last_commit_date: 2024-12-16 16:40:09 -0500 (Mon, 16 Dec 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  YES
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  YES
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  YES
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  YES


CHECK results for SOMNiBUS on kjohnson1

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: 1.14.2
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_1.14.2.tar.gz
StartedAt: 2024-12-21 10:00:36 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 10:23:44 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 1387.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SOMNiBUS.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running 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_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SOMNiBUS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SOMNiBUS/DESCRIPTION’ ... OK
* this is package ‘SOMNiBUS’ version ‘1.14.2’
* 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 ... NOTE
testStat: no visible global function definition for ‘pf’
Undefined global functions or variables:
  pf
Consider adding
  importFrom("stats", "pf")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'formatFromBSseq.Rd':
  ‘formatFromBSmooth’

Missing link or links in Rd file 'formatFromBismark.Rd':
  ‘formatFromBSmooth’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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     431.175 16.844 451.917
runSOMNiBUS           357.615 20.142 379.995
binomRegMethPredPlot   41.810  3.959  46.559
binomRegMethModelPlot  40.929  4.020  45.173
binomRegMethModelPred  39.467  4.586  44.454
splitDataByGene        14.588  1.172  16.016
splitDataByChromatin    9.580  0.341  11.576
formatFromBismark       5.887  0.399   6.140
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SOMNiBUS.Rcheck/00check.log’
for details.


Installation output

SOMNiBUS.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘SOMNiBUS’ ...
** 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
binomRegMethModel431.175 16.844451.917
binomRegMethModelPlot40.929 4.02045.173
binomRegMethModelPred39.467 4.58644.454
binomRegMethModelSim2.3040.2222.544
binomRegMethPredPlot41.810 3.95946.559
formatFromBSseq0.1260.0010.128
formatFromBismark5.8870.3996.140
runSOMNiBUS357.615 20.142379.995
splitDataByChromatin 9.580 0.34111.576
splitDataByDensity3.7350.1123.852
splitDataByGRanges0.1920.0150.207
splitDataByGene14.588 1.17216.016
splitDataByRegion0.0170.0030.019