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This page was generated on 2024-04-18 11:32:15 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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 1428/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 2.34.0  (landing page)
Alba Sala
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/nucleR
git_branch: RELEASE_3_18
git_last_commit: 49b3021
git_last_commit_date: 2023-10-24 09:47:23 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for nucleR on kjohnson1


To the developers/maintainers of the nucleR package:
- 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: 2.34.0
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_2.34.0.tar.gz
StartedAt: 2024-04-17 21:39:29 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 21:44:44 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 314.8 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_2.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/nucleR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nucleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nucleR’ version ‘2.34.0’
* 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 ‘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 R 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 documentation object '.fftRegion'
  ‘data2’ ‘pcKeepComp’

Undocumented arguments in documentation object '.loadFiles'
  ‘singleLoad’ ‘pairedLoad’

Undocumented arguments in documentation object '.loadPairedBam'
  ‘file’

Undocumented arguments in documentation object '.loadSingleBam'
  ‘exp’

Undocumented arguments in documentation object '.mid'
  ‘x’

Undocumented arguments in documentation object '.unlist_as_integer'
  ‘x’

Undocumented arguments in documentation object '.xlapply'
  ‘X’ ‘FUN’ ‘...’ ‘mc.cores’

Documented arguments not in \usage in documentation object 'pcKeepCompDetect':
  ‘...’

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 35.488  0.604  36.172
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc-mac-arm64/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
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘nucleR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Loading required package: usethis

Welcome at Tue Apr 16 10:58:32 2024 

Goodbye at  Tue Apr 16 10:58:45 2024 
** help
*** installing help indices
** building package indices
Loading required package: usethis

Welcome at Tue Apr 16 10:58:47 2024 

Goodbye at  Tue Apr 16 10:58:47 2024 
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: usethis

Welcome at Tue Apr 16 10:58:48 2024 

Goodbye at  Tue Apr 16 10:59:00 2024 
** testing if installed package can be loaded from final location
Loading required package: usethis

Welcome at Tue Apr 16 10:59:02 2024 

Goodbye at  Tue Apr 16 10:59:14 2024 
** testing if installed package keeps a record of temporary installation path
* DONE (nucleR)

Tests output

nucleR.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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 
 13.368   0.481  14.032 

Example timings

nucleR.Rcheck/nucleR-Ex.timings

nameusersystemelapsed
controlCorrection0.0750.0070.082
coverage.rpm0.5250.0180.542
export.bed0.1780.0100.191
export.wig0.0460.0700.120
filterFFT1.4590.0221.496
fragmentLenDetect0.5650.0520.618
mergeCalls0.5160.0230.538
nucleR-package1.4810.0531.539
pcKeepCompDetect0.3070.0110.319
peakDetection1.3350.0681.403
peakScoring0.3780.0160.395
plotPeaks1.0560.0171.073
processReads0.3340.0140.348
processTilingArray0.0000.0010.000
readBAM0.1250.0040.131
syntheticNucMap35.488 0.60436.172