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This page was generated on 2023-01-02 09:00:41 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the nucleR package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1352/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 2.31.0  (landing page)
Alba Sala
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/nucleR
git_branch: master
git_last_commit: b03e676
git_last_commit_date: 2022-11-01 11:06:05 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

Summary

Package: nucleR
Version: 2.31.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nucleR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings nucleR_2.31.0.tar.gz
StartedAt: 2022-12-29 01:54:20 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 01:58:08 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 227.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: nucleR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nucleR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings nucleR_2.31.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/nucleR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '2.31.0'
* 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 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 30.83   0.37    31.2
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/nucleR.Rcheck/00check.log'
for details.



Installation output

nucleR.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL nucleR
###
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* installing to library 'F:/biocbuild/bbs-3.17-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 Dec 28 15:59:12 2022 

Goodbye at  Wed Dec 28 15:59:22 2022 
** help
*** installing help indices
** building package indices
Loading required package: usethis

Welcome at Wed Dec 28 15:59:24 2022 

Goodbye at  Wed Dec 28 15:59:25 2022 
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: usethis

Welcome at Wed Dec 28 15:59:26 2022 

Goodbye at  Wed Dec 28 15:59:34 2022 
** testing if installed package can be loaded from final location
Loading required package: usethis

Welcome at Wed Dec 28 15:59:36 2022 

Goodbye at  Wed Dec 28 15:59:44 2022 
** testing if installed package keeps a record of temporary installation path
* DONE (nucleR)

Tests output

nucleR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   8.03    0.40    8.40 

Example timings

nucleR.Rcheck/nucleR-Ex.timings

nameusersystemelapsed
controlCorrection0.130.000.12
coverage.rpm0.420.050.50
export.bed0.070.030.12
export.wig0.070.080.14
filterFFT1.150.031.19
fragmentLenDetect0.470.030.50
mergeCalls0.630.000.62
nucleR-package1.390.071.46
pcKeepCompDetect0.390.010.40
peakDetection1.120.021.14
peakScoring0.270.010.29
plotPeaks0.910.000.91
processReads0.280.000.28
processTilingArray000
readBAM0.080.000.10
syntheticNucMap30.83 0.3731.20