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This page was generated on 2025-08-09 12:08 -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 1449/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 2.41.1  (landing page)
Alba Sala
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/nucleR
git_branch: devel
git_last_commit: 29c0c53
git_last_commit_date: 2025-07-22 13:46:37 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for nucleR on lconway

To the developers/maintainers of the nucleR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nucleR.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: nucleR
Version: 2.41.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nucleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nucleR_2.41.1.tar.gz
StartedAt: 2025-08-08 22:46:40 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 22:52:02 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 321.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: nucleR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nucleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nucleR_2.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/nucleR.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 ‘nucleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nucleR’ version ‘2.41.1’
* 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 ‘nucleR’ 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 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 ... NOTE
Unknown package ‘Starr’ in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'dot-fftRegion.Rd'
  ‘data2’ ‘pcKeepComp’

Undocumented arguments in Rd file 'dot-loadFiles.Rd'
  ‘singleLoad’ ‘pairedLoad’

Undocumented arguments in Rd file 'dot-loadPairedBam.Rd'
  ‘file’

Undocumented arguments in Rd file 'dot-loadSingleBam.Rd'
  ‘exp’

Undocumented arguments in Rd file 'dot-mid.Rd'
  ‘x’

Undocumented arguments in Rd file 'dot-unlist_as_integer.Rd'
  ‘x’

Undocumented arguments in Rd file 'dot-xlapply.Rd'
  ‘X’ ‘FUN’ ‘...’ ‘mc.cores’

Documented arguments not in \usage in Rd file 'pcKeepCompDetect.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
syntheticNucMap 42.251  0.535  43.079
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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-3.22-bioc/meat/nucleR.Rcheck/00check.log’
for details.


Installation output

nucleR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘nucleR’ ...
** this is package ‘nucleR’ version ‘2.41.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Loading required package: usethis

Welcome at Fri Aug  8 15:40:52 2025 

Goodbye at  Fri Aug  8 15:41:07 2025 
** help
*** installing help indices
** building package indices
Loading required package: usethis

Welcome at Fri Aug  8 15:41:09 2025 

Goodbye at  Fri Aug  8 15:41:09 2025 
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: usethis

Welcome at Fri Aug  8 15:41:11 2025 

Goodbye at  Fri Aug  8 15:41:24 2025 
** testing if installed package can be loaded from final location
Loading required package: usethis

Welcome at Fri Aug  8 15:41:26 2025 

Goodbye at  Fri Aug  8 15:41:39 2025 
** testing if installed package keeps a record of temporary installation path
* DONE (nucleR)

Tests output

nucleR.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(nucleR)
> 
> test_check("nucleR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 11.837   0.600  12.520 

Example timings

nucleR.Rcheck/nucleR-Ex.timings

nameusersystemelapsed
controlCorrection0.0910.0100.102
coverage.rpm0.4400.0460.491
export.bed0.2150.0150.230
export.wig0.0490.0780.128
filterFFT0.6360.0260.673
fragmentLenDetect0.6250.0370.666
mergeCalls0.6240.0080.635
nucleR-package1.8940.0301.935
pcKeepCompDetect0.3800.0090.391
peakDetection1.8620.0441.923
peakScoring1.1990.0221.230
plotPeaks1.3870.0281.426
processReads0.3630.0160.383
processTilingArray0.0010.0010.000
readBAM0.1290.0050.136
syntheticNucMap42.251 0.53543.079