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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:regioneReloaded.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings regioneReloaded_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/regioneReloaded.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 ‘regioneReloaded/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneReloaded’ version ‘1.11.0’
* 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 ‘regioneReloaded’ 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 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:
  AlienRSList_broad.Rd: createRandomRegions
  AlienRSList_narrow.Rd: createRandomRegions
  makeLZMatrix.Rd: localZScore
  plotCrosswiseDimRed.Rd: pam, geom_text_repel, Rtsne
  plotCrosswiseMatrix.Rd: geom_raster
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
crosswisePermTest 15.551  0.188  15.742
multiLocalZscore   6.456  0.076   6.532
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/regioneReloaded.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL regioneReloaded
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘regioneReloaded’ ...
** this is package ‘regioneReloaded’ version ‘1.11.0’
** using staged installation
** R
** data
** 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 (regioneReloaded)

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(regioneReloaded)
Loading required package: 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("regioneReloaded")
[1] "method selected for hclustering: average"
 complete   average    single   ward.D2    median  centroid  mcquitty 
0.7497654 0.7857181 0.6514804 0.7363304 0.3459672 0.4561003 0.7516609 
[1] "method selected for hclustering: complete"
 complete   average    single   ward.D2    median  centroid  mcquitty 
0.9098230 0.8541174 0.7986368 0.8320493 0.8348816 0.8510903 0.8475492 
[1] "method selected for hclustering: average"
 complete   average    single   ward.D2    median  centroid  mcquitty 
0.8909663 0.8944326 0.7892161 0.8311822 0.8813696 0.8857083 0.8784679 
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "method selected for hclustering: average"
 complete   average    single   ward.D2    median  centroid  mcquitty 
0.7515325 0.7716179 0.6542890 0.7136237 0.2223408 0.5618311 0.7245865 
[1] "method selected for hclustering: average"
 complete   average    single   ward.D2    median  centroid  mcquitty 
0.7497654 0.7857181 0.6514804 0.7363304 0.3459672 0.4561003 0.7516609 
[1] "method selected for hclustering: complete"
 complete   average    single   ward.D2    median  centroid  mcquitty 
0.9098230 0.8541174 0.7986368 0.8320493 0.8348816 0.8510903 0.8475492 
[1] "method selected for hclustering: average"
 complete   average    single   ward.D2    median  centroid  mcquitty 
0.8909663 0.8944326 0.7892161 0.8311822 0.8813696 0.8857083 0.8784679 
[ FAIL 0 | WARN 132 | SKIP 6 | PASS 60 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-crosswisePermTest.R:9:3', 'test-crosswisePermTest.R:67:3',
  'test-crosswisePermTest.R:99:3', 'test-getMatrix.R:6:3',
  'test-getMultiEvaluation.R:2:3', 'test-getParameters.R:7:3'

[ FAIL 0 | WARN 132 | SKIP 6 | PASS 60 ]
> 
> proc.time()
   user  system elapsed 
170.975  19.288 120.040