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This page was generated on 2025-10-20 12:04 -0400 (Mon, 20 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1753/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.41.3  (landing page)
Bernat Gel
Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 Oct 2025)
git_url: https://git.bioconductor.org/packages/regioneR
git_branch: devel
git_last_commit: 140bec6
git_last_commit_date: 2025-06-21 01:57:42 -0400 (Sat, 21 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    TIMEOUT  skipped


CHECK results for regioneR on nebbiolo2

To the developers/maintainers of the regioneR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/regioneR.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: regioneR
Version: 1.41.3
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings regioneR_1.41.3.tar.gz
StartedAt: 2025-10-20 03:51:13 -0400 (Mon, 20 Oct 2025)
EndedAt: 2025-10-20 03:59:16 -0400 (Mon, 20 Oct 2025)
EllapsedTime: 482.5 seconds
RetCode: 0
Status:   OK  
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings regioneR_1.41.3.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/regioneR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘regioneR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneR’ version ‘1.41.3’
* 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 ‘regioneR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicRanges’
A package should be listed in only one of these fields.
* 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 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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  characterToBSGenome.Rd: BSgenome
  circularRandomizeRegions.Rd: GenomicRanges, BSgenome
  commonRegions.Rd: GenomicRanges
  createRandomRegions.Rd: GenomicRanges, BSgenome
  extendRegions.Rd: GenomicRanges
  filterChromosomes.Rd: GenomicRanges, BSgenome, GRanges
  getGenome.Rd: BSgenome, GRanges, memoise, forget
  getGenomeAndMask.Rd: BSgenome, memoise, forget
  getMask.Rd: BSgenome, GRanges, memoise, forget
  joinRegions.Rd: GenomicRanges, reduce
  localZScore.Rd: GenomicRanges
  maskFromBSGenome.Rd: BSgenome, GRanges, memoise, forget
  meanDistance.Rd: GenomicRanges
  meanInRegions.Rd: GenomicRanges
  mergeRegions.Rd: GenomicRanges, reduce
  numOverlaps.Rd: GenomicRanges
  overlapGraphicalSummary.Rd: GenomicRanges
  overlapPermTest.Rd: GenomicRanges
  overlapRegions.Rd: GenomicRanges, countOverlaps
  permTest.Rd: GenomicRanges
  randomizeRegions.Rd: GenomicRanges, BSgenome
  resampleGenome.Rd: GenomicRanges
  resampleRegions.Rd: GenomicRanges
  splitRegions.Rd: GenomicRanges
  subtractRegions.Rd: GenomicRanges
  toDataframe.Rd: GRanges
  toGRanges.Rd: GRanges, BSgenome
  uniqueRegions.Rd: GenomicRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
circularRandomizeRegions 30.995  4.570  35.652
maskFromBSGenome         29.078  5.542  32.660
filterChromosomes        28.824  4.265  33.091
getMask                  27.037  4.007  31.046
resampleGenome            7.697  0.483   8.179
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/regioneR.Rcheck/00check.log’
for details.


Installation output

regioneR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL regioneR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘regioneR’ ...
** this is package ‘regioneR’ version ‘1.41.3’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (regioneR)

Tests output

regioneR.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(regioneR)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
> 
> test_check("regioneR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
> 
> proc.time()
   user  system elapsed 
 43.972   5.184  49.150 

Example timings

regioneR.Rcheck/regioneR-Ex.timings

nameusersystemelapsed
characterToBSGenome0.1140.0090.123
circularRandomizeRegions30.995 4.57035.652
commonRegions0.2590.0000.258
createFunctionsList0.4190.0000.418
createRandomRegions0.1840.0010.184
emptyCacheRegioneR0.0010.0000.000
extendRegions0.1170.0010.118
filterChromosomes28.824 4.26533.091
getChromosomesByOrganism0.0010.0000.000
getGenome0.1850.0010.186
getGenomeAndMask0.0420.0000.043
getMask27.037 4.00731.046
joinRegions0.1110.0000.112
listChrTypes0.0070.0000.007
localZScore3.1080.4794.447
maskFromBSGenome29.078 5.54232.660
meanDistance0.0720.0050.076
meanInRegions0.1060.0040.110
mergeRegions0.0830.0020.085
numOverlaps0.1520.0100.162
overlapGraphicalSummary0.0810.0000.082
overlapPermTest1.5410.0611.603
overlapRegions0.0390.0000.038
permTest1.1120.0091.121
plot.localZScoreResults1.1860.0071.193
plot.localZScoreResultsList2.4780.0332.511
plot.permTestResults1.8110.0901.901
plot.permTestResultsList1.9680.0191.988
plotRegions0.0380.0000.038
print.permTestResults1.1080.0041.112
randomizeRegions0.2040.0060.210
recomputePermTest0.7660.0040.770
resampleGenome7.6970.4838.179
resampleRegions0.0370.0000.036
splitRegions0.0650.0000.065
subtractRegions0.1480.0010.150
toDataframe0.0150.0010.016
toGRanges0.6100.0150.625
uniqueRegions0.3040.0020.306