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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:regioneReloaded.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings regioneReloaded_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/regioneReloaded.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘regioneReloaded/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneReloaded’ version ‘1.1.0’
* 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 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 ... OK
* 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      23.180  0.110  23.653
multiLocalZscore        9.779  0.008  10.350
multiLocalZScore-class  4.980  0.008   5.221
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Loading required package: GenomeInfoDb
  > 
  > 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"
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘regioneReloaded.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘regioneReloaded.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/regioneReloaded.Rcheck/vign_test/regioneReloaded/vignettes/regioneReloaded_files/figure-html/unnamed-chunk-3-1.png" but not available.
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/regioneReloaded.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL regioneReloaded
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘regioneReloaded’ ...
** 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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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.

> # 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> 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"
Killed