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This page was generated on 2024-06-21 17:39 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1444/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 2.36.0  (landing page)
Alba Sala
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/nucleR
git_branch: RELEASE_3_19
git_last_commit: df2686d
git_last_commit_date: 2024-04-30 10:25:01 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for nucleR on palomino3

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: 2.36.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nucleR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings nucleR_2.36.0.tar.gz
StartedAt: 2024-06-20 08:22:59 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 08:32:16 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 556.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: nucleR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nucleR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings nucleR_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/nucleR.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'nucleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nucleR' version '2.36.0'
* 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 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 40.33    0.5   40.83
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/nucleR.Rcheck/00check.log'
for details.


Installation output

nucleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL nucleR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 Wed Jun 19 16:06:07 2024 

Goodbye at  Wed Jun 19 16:06:22 2024 
** help
*** installing help indices
** building package indices
Loading required package: usethis

Welcome at Wed Jun 19 16:06:32 2024 

Goodbye at  Wed Jun 19 16:06:33 2024 
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: usethis

Welcome at Wed Jun 19 16:06:35 2024 

Goodbye at  Wed Jun 19 16:06:46 2024 
** testing if installed package can be loaded from final location
Loading required package: usethis

Welcome at Wed Jun 19 16:06:48 2024 

Goodbye at  Wed Jun 19 16:06:59 2024 
** testing if installed package keeps a record of temporary installation path
* DONE (nucleR)

Tests output

nucleR.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   9.46    9.65   19.21 

Example timings

nucleR.Rcheck/nucleR-Ex.timings

nameusersystemelapsed
controlCorrection0.080.010.09
coverage.rpm0.390.130.68
export.bed0.221.251.55
export.wig0.030.080.10
filterFFT0.560.060.63
fragmentLenDetect0.561.322.00
mergeCalls0.520.000.52
nucleR-package1.800.061.87
pcKeepCompDetect0.280.050.33
peakDetection3.000.073.08
peakScoring0.450.020.47
plotPeaks1.110.081.18
processReads1.060.041.11
processTilingArray000
readBAM0.110.000.14
syntheticNucMap40.33 0.5040.83