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This page was generated on 2023-04-12 11:05:12 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for nucleR on nebbiolo2


To the developers/maintainers of the nucleR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1367/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 2.30.0  (landing page)
Alba Sala
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/nucleR
git_branch: RELEASE_3_16
git_last_commit: 8697d8d
git_last_commit_date: 2022-11-01 11:06:05 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: nucleR
Version: 2.30.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:nucleR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings nucleR_2.30.0.tar.gz
StartedAt: 2023-04-10 22:24:11 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 22:29:24 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 312.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: nucleR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:nucleR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings nucleR_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/nucleR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘nucleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nucleR’ version ‘2.30.0’
* 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 loading without being on the library search path ... 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 36.68  0.643  37.325
* 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 ...
  ‘nucleR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/nucleR.Rcheck/00check.log’
for details.



Installation output

nucleR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL nucleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 Mon Apr 10 15:31:31 2023 

Goodbye at  Mon Apr 10 15:31:46 2023 
** help
*** installing help indices
** building package indices
Loading required package: usethis

Welcome at Mon Apr 10 15:31:48 2023 

Goodbye at  Mon Apr 10 15:31:48 2023 
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: usethis

Welcome at Mon Apr 10 15:31:49 2023 

Goodbye at  Mon Apr 10 15:32:01 2023 
** testing if installed package can be loaded from final location
Loading required package: usethis

Welcome at Mon Apr 10 15:32:02 2023 

Goodbye at  Mon Apr 10 15:32:14 2023 
** testing if installed package keeps a record of temporary installation path
* DONE (nucleR)

Tests output

nucleR.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  8.785   0.544   9.311 

Example timings

nucleR.Rcheck/nucleR-Ex.timings

nameusersystemelapsed
controlCorrection0.0630.0170.080
coverage.rpm1.2060.1041.310
export.bed0.1530.0030.155
export.wig0.0310.0310.062
filterFFT0.5770.0120.589
fragmentLenDetect0.5410.0110.553
mergeCalls0.5480.0000.548
nucleR-package1.4100.0441.454
pcKeepCompDetect0.3410.0040.344
peakDetection1.5220.0721.594
peakScoring0.3830.0000.383
plotPeaks1.1980.0471.247
processReads0.3250.0200.345
processTilingArray000
readBAM0.1380.0080.147
syntheticNucMap36.680 0.64337.325