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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings regioneR_1.43.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/regioneR.Rcheck’
* using R Under development (unstable) (2025-12-18 r89199)
* 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 ‘1.43.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Bernat Gel <bgel@imppc.org>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Anna",
                      family = "Diez-Villanueva",
                      role = "aut",
                      email = "adiez@iconcologia.net"),
               person(given = "Roberto",
                      family = "Malinverni",
                      role = "aut",
                      email = "roberto.malinverni@gmail.com"),
               person(given = "Bernat",
                      family = "Gel",
                      role = c("aut", "cre"),
                      email = "bgel@igtp.cat"))
as necessary.

The Title field should be in title case. Current version is:
  ‘Association analysis of genomic regions based on permutation tests’
In title case that is:
  ‘Association Analysis of Genomic Regions Based on Permutation Tests’

The Description field should not start with the package name,
  'This package' or similar.

The Date field is over a month old.
* 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 use of S3 registration ... 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 ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
circularRandomizeRegions 20.912  4.779  25.704
maskFromBSGenome         19.823  5.029  23.409
filterChromosomes        19.926  4.364  24.301
getMask                  18.668  4.518  23.192
resampleGenome            5.619  0.409   6.031
* 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: 4 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/regioneR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL regioneR
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘regioneR’ ...
** this is package ‘regioneR’ version ‘1.43.0’
** 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)

R Under development (unstable) (2025-12-18 r89199) -- "Unsuffered Consequences"
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 2 | PASS 89 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): ,

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 89 ]
> 
> proc.time()
   user  system elapsed 
 31.457   5.025  36.480