##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:peakCombiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings peakCombiner_0.99.603.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/peakCombiner.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘peakCombiner/DESCRIPTION’ ... OK
* this is package ‘peakCombiner’ version ‘0.99.603’
* 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 ‘peakCombiner’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL peakCombiner
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘peakCombiner’ ...
** this is package ‘peakCombiner’ version ‘0.99.603’
** using staged installation
** R
** data
** 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 (peakCombiner)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(peakCombiner)
> 
> test_check("peakCombiner")
ℹ Argument `outputFormat` is set to "tibble".
ℹ Argument `startsAreBased` is 1.
ℹ Argument `starts.in.df.are.0based` is FALSE.
ℹ Provide input `data` is a pre-loaded <data.frame> with the required column
  names.
→ Start preparing data.
ℹ Required columns will be added if missing.
! Column 'score' does not exist in `data_prepared`.
→ Column 'score' is added and filled with "0".
! Column 'strand' does not exist in `data_prepared`.
→ Column 'strand' is added and filled with ".".
! Column 'summit' does not exist in `data_prepared`.
→ As no input column 'summit' is found, the output column 'center' has to be
  filled with arithmetic center of peak.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Checking whether duplicated regions exist and need to be collapsed.
→ Checked whether duplicated regions exist and need to be collapsed.
✔ Duplicated regions identified and collapsed to unique chrom, start, and end
  for each sample by strongest score value.
  
✔ Preparation of data finished successfully.
ℹ Output format is set to "tibble".
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     441   458 control_rep1|9      0 .         450 control_rep1
 2 chr1     641   658 control_rep1|1      0 .         650 control_rep1
 3 chr1    3941  3958 control_rep1|2      0 .        3950 control_rep1
 4 chr1    4991  5008 control_rep1|4      0 .        5000 control_rep1
 5 chr1    5841  5858 control_rep1|5      0 .        5850 control_rep1
 6 chr1    7041  7058 control_rep1|6      0 .        7050 control_rep1
 7 chr10    641   658 control_rep1|7      0 .         650 control_rep1
 8 chr2     641   658 control_rep1|8      0 .         650 control_rep1
 9 chr4 2   641   658 control_rep1|10     0 .         650 control_rep1
10 chr4-2   741   758 control_rep1|11     0 .         750 control_rep1
# ℹ 41 more rows
# A tibble: 42 × 8
   chrom start   end name           score strand center sample_name 
   <chr> <int> <int> <chr>          <dbl> <chr>   <dbl> <chr>       
 1 chr1    559   738 control_rep1|1     0 .         650 control_rep1
 2 chr1   3859  4038 control_rep1|2     0 .        3950 control_rep1
 3 chr1   4909  5088 control_rep1|4     0 .        5000 control_rep1
 4 chr1   5759  5938 control_rep1|5     0 .        5850 control_rep1
 5 chr1   6959  7138 control_rep1|6     0 .        7050 control_rep1
 6 chr10   559   738 control_rep1|7     0 .         650 control_rep1
 7 chr2    559   738 control_rep1|8     0 .         650 control_rep1
 8 chr1    109   288 control_rep2|1     0 .         200 control_rep2
 9 chr1    509   688 control_rep2|2     0 .         600 control_rep2
10 chr1   3759  3938 control_rep2|3     0 .        3850 control_rep2
# ℹ 32 more rows
# A tibble: 8 × 8
  chrom start   end name       score strand center sample_name
  <chr> <int> <int> <chr>      <dbl> <chr>   <dbl> <chr>      
1 chr1    498   701 combined|1     0 .         600 combined   
2 chr1   2798  3001 combined|2     0 .        2900 combined   
3 chr1   3848  4051 combined|3     0 .        3950 combined   
4 chr1   4798  5001 combined|4     0 .        4900 combined   
5 chr1   5948  6151 combined|5     0 .        6050 combined   
6 chr1   6948  7151 combined|6     0 .        7050 combined   
7 chr2    448   651 combined|7     0 .         550 combined   
8 chr10   448   651 combined|8     0 .         550 combined   
# A tibble: 42 x 8
   chrom start   end name           score strand center sample_name 
   <chr> <int> <int> <chr>          <dbl> <chr>   <dbl> <chr>       
 1 chr1    300   999 control_rep1|1     0 .         650 control_rep1
 2 chr1   3600  4299 control_rep1|2     0 .        3950 control_rep1
 3 chr1   4650  5349 control_rep1|4     0 .        5000 control_rep1
 4 chr1   5500  6199 control_rep1|5     0 .        5850 control_rep1
 5 chr1   6700  7399 control_rep1|6     0 .        7050 control_rep1
 6 chr10   300   999 control_rep1|7     0 .         650 control_rep1
 7 chr2    300   999 control_rep1|8     0 .         650 control_rep1
 8 chr1      1   549 control_rep2|1     0 .         200 control_rep2
 9 chr1    250   949 control_rep2|2     0 .         600 control_rep2
10 chr1   3500  4199 control_rep2|3     0 .        3850 control_rep2
# i 32 more rows
# A tibble: 42 x 8
   chrom start   end name           score strand center sample_name 
   <chr> <int> <int> <chr>          <dbl> <chr>   <dbl> <chr>       
 1 chr1    300   999 control_rep1|1     0 .         650 control_rep1
 2 chr1   3600  4299 control_rep1|2     0 .        3950 control_rep1
 3 chr1   4650  5349 control_rep1|4     0 .        5000 control_rep1
 4 chr1   5500  6199 control_rep1|5     0 .        5850 control_rep1
 5 chr1   6700  7399 control_rep1|6     0 .        7050 control_rep1
 6 chr10   300   999 control_rep1|7     0 .         650 control_rep1
 7 chr2    300   999 control_rep1|8     0 .         650 control_rep1
 8 chr1      1   549 control_rep2|1     0 .         200 control_rep2
 9 chr1    250   949 control_rep2|2     0 .         600 control_rep2
10 chr1   3500  4199 control_rep2|3     0 .        3850 control_rep2
# i 32 more rows
# A tibble: 51 x 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     100   799 control_rep1|9      0 .         450 control_rep1
 2 chr1     300   999 control_rep1|1      0 .         650 control_rep1
 3 chr1    3600  4299 control_rep1|2      0 .        3950 control_rep1
 4 chr1    4650  5349 control_rep1|4      0 .        5000 control_rep1
 5 chr1    5500  6199 control_rep1|5      0 .        5850 control_rep1
 6 chr1    6700  7399 control_rep1|6      0 .        7050 control_rep1
 7 chr10    300   999 control_rep1|7      0 .         650 control_rep1
 8 chr2     300   999 control_rep1|8      0 .         650 control_rep1
 9 chr4 2   300   999 control_rep1|10     0 .         650 control_rep1
10 chr4-2   400  1099 control_rep1|11     0 .         750 control_rep1
# i 41 more rows
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "350".
i Genomic regions will be expanded by 350bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Starting with expanding genomic regions from the column center.
> Genomic regions will be centered and expanded.
i Used genome for trimming is NA.
> Expanding genomic regions from the column center by 350 before and 350 after the center.
# A tibble: 51 x 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     100   799 control_rep1|9      0 .         450 control_rep1
 2 chr1     300   999 control_rep1|1      0 .         650 control_rep1
 3 chr1    3600  4299 control_rep1|2      0 .        3950 control_rep1
 4 chr1    4650  5349 control_rep1|4      0 .        5000 control_rep1
 5 chr1    5500  6199 control_rep1|5      0 .        5850 control_rep1
 6 chr1    6700  7399 control_rep1|6      0 .        7050 control_rep1
 7 chr10    300   999 control_rep1|7      0 .         650 control_rep1
 8 chr2     300   999 control_rep1|8      0 .         650 control_rep1
 9 chr4 2   300   999 control_rep1|10     0 .         650 control_rep1
10 chr4-2   400  1099 control_rep1|11     0 .         750 control_rep1
# i 41 more rows
v Genomic regions were successfully centered and expanded.
  
v Genomic regions were successfully centered and expanded.
  
i Output format is set to "tibble".
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "102".
i Genomic regions will be expanded by 102bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Starting with expanding genomic regions from the column center.
> Genomic regions will be centered and expanded.
i Used genome for trimming is NA.
> Expanding genomic regions from the column center by 102 before and 102 after the center.
# A tibble: 8 x 8
  chrom start   end name       score strand center sample_name
  <chr> <int> <int> <chr>      <dbl> <chr>   <dbl> <chr>      
1 chr1    498   701 combined|1     0 .         600 combined   
2 chr1   2798  3001 combined|2     0 .        2900 combined   
3 chr1   3848  4051 combined|3     0 .        3950 combined   
4 chr1   4798  5001 combined|4     0 .        4900 combined   
5 chr1   5948  6151 combined|5     0 .        6050 combined   
6 chr1   6948  7151 combined|6     0 .        7050 combined   
7 chr2    448   651 combined|7     0 .         550 combined   
8 chr10   448   651 combined|8     0 .         550 combined   
v Genomic regions were successfully centered and expanded.
  
v Genomic regions were successfully centered and expanded.
  
i Output format is set to "tibble".
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "350".
i Genomic regions will be expanded by 350bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Starting with expanding genomic regions from the column center.
> Genomic regions will be centered and expanded.
i Used genome for trimming is NA.
> Expanding genomic regions from the column center by 350 before and 350 after the center.
# A tibble: 51 x 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     100   799 control_rep1|9      0 .         450 control_rep1
 2 chr1     300   999 control_rep1|1      0 .         650 control_rep1
 3 chr1    3600  4299 control_rep1|2      0 .        3950 control_rep1
 4 chr1    4650  5349 control_rep1|4      0 .        5000 control_rep1
 5 chr1    5500  6199 control_rep1|5      0 .        5850 control_rep1
 6 chr1    6700  7399 control_rep1|6      0 .        7050 control_rep1
 7 chr10    300   999 control_rep1|7      0 .         650 control_rep1
 8 chr2     300   999 control_rep1|8      0 .         650 control_rep1
 9 chr4 2   300   999 control_rep1|10     0 .         650 control_rep1
10 chr4-2   400  1099 control_rep1|11     0 .         750 control_rep1
# i 41 more rows
v Genomic regions were successfully centered and expanded.
  
v Genomic regions were successfully centered and expanded.
  
i Output format is set to "tibble".
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "350".
i Genomic regions will be expanded by 350bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "350".
i Genomic regions will be expanded by 350bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "350".
i Genomic regions will be expanded by 350bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "350".
i Genomic regions will be expanded by 350bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "350".
i Genomic regions will be expanded by 350bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Starting with expanding genomic regions from the column center.
> Genomic regions will be centered and expanded.
i Used genome for trimming is NA.
> Expanding genomic regions from the column center by 350 before and 350 after the center.
# A tibble: 51 x 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     100   799 control_rep1|9      0 .         450 control_rep1
 2 chr1     300   999 control_rep1|1      0 .         650 control_rep1
 3 chr1    3600  4299 control_rep1|2      0 .        3950 control_rep1
 4 chr1    4650  5349 control_rep1|4      0 .        5000 control_rep1
 5 chr1    5500  6199 control_rep1|5      0 .        5850 control_rep1
 6 chr1    6700  7399 control_rep1|6      0 .        7050 control_rep1
 7 chr10    300   999 control_rep1|7      0 .         650 control_rep1
 8 chr2     300   999 control_rep1|8      0 .         650 control_rep1
 9 chr4 2   300   999 control_rep1|10     0 .         650 control_rep1
10 chr4-2   400  1099 control_rep1|11     0 .         750 control_rep1
# i 41 more rows
v Genomic regions were successfully centered and expanded.
  
v Genomic regions were successfully centered and expanded.
  
i Output format is set to "tibble".
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "350".
i Genomic regions will be expanded by 350bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Starting with expanding genomic regions from the column center.
> Genomic regions will be centered and expanded.
i Used genome for trimming is NA.
> Expanding genomic regions from the column center by 350 before and 350 after the center.
# A tibble: 51 x 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     100   799 control_rep1|9      0 .         450 control_rep1
 2 chr1     300   999 control_rep1|1      0 .         650 control_rep1
 3 chr1    3600  4299 control_rep1|2      0 .        3950 control_rep1
 4 chr1    4650  5349 control_rep1|4      0 .        5000 control_rep1
 5 chr1    5500  6199 control_rep1|5      0 .        5850 control_rep1
 6 chr1    6700  7399 control_rep1|6      0 .        7050 control_rep1
 7 chr10    300   999 control_rep1|7      0 .         650 control_rep1
 8 chr2     300   999 control_rep1|8      0 .         650 control_rep1
 9 chr4 2   300   999 control_rep1|10     0 .         650 control_rep1
10 chr4-2   400  1099 control_rep1|11     0 .         750 control_rep1
# i 41 more rows
v Genomic regions were successfully centered and expanded.
  
v Genomic regions were successfully centered and expanded.
  
i Output format is set to "tibble".
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "350".
i Genomic regions will be expanded by 350bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Starting with expanding genomic regions from the column center.
> Genomic regions will be centered and expanded.
i Used genome for trimming is NA.
> Expanding genomic regions from the column center by 350 before and 350 after the center.
# A tibble: 51 x 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     100   799 control_rep1|9      0 .         450 control_rep1
 2 chr1     300   999 control_rep1|1      0 .         650 control_rep1
 3 chr1    3600  4299 control_rep1|2      0 .        3950 control_rep1
 4 chr1    4650  5349 control_rep1|4      0 .        5000 control_rep1
 5 chr1    5500  6199 control_rep1|5      0 .        5850 control_rep1
 6 chr1    6700  7399 control_rep1|6      0 .        7050 control_rep1
 7 chr10    300   999 control_rep1|7      0 .         650 control_rep1
 8 chr2     300   999 control_rep1|8      0 .         650 control_rep1
 9 chr4 2   300   999 control_rep1|10     0 .         650 control_rep1
10 chr4-2   400  1099 control_rep1|11     0 .         750 control_rep1
# i 41 more rows
v Genomic regions were successfully centered and expanded.
  
v Genomic regions were successfully centered and expanded.
  
i Output format is set to "tibble".
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "90".
i Genomic regions will be expanded by 90bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Starting with expanding genomic regions from the column center.
> Genomic regions will be centered and expanded.
i Used genome for trimming is NA.
> Expanding genomic regions from the column center by 90 before and 90 after the center.
# A tibble: 42 x 8
   chrom start   end name           score strand center sample_name 
   <chr> <int> <int> <chr>          <dbl> <chr>   <dbl> <chr>       
 1 chr1    560   739 control_rep1|1     0 .         650 control_rep1
 2 chr1   3860  4039 control_rep1|2     0 .        3950 control_rep1
 3 chr1   4910  5089 control_rep1|4     0 .        5000 control_rep1
 4 chr1   5760  5939 control_rep1|5     0 .        5850 control_rep1
 5 chr1   6960  7139 control_rep1|6     0 .        7050 control_rep1
 6 chr10   560   739 control_rep1|7     0 .         650 control_rep1
 7 chr2    560   739 control_rep1|8     0 .         650 control_rep1
 8 chr1    110   289 control_rep2|1     0 .         200 control_rep2
 9 chr1    510   689 control_rep2|2     0 .         600 control_rep2
10 chr1   3760  3939 control_rep2|3     0 .        3850 control_rep2
# i 32 more rows
v Genomic regions were successfully centered and expanded.
  
v Genomic regions were successfully centered and expanded.
  
i Output format is set to "tibble".
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "90".
i Genomic regions will be expanded by 90bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Starting with expanding genomic regions from the column center.
> Genomic regions will be centered and expanded.
i Used genome for trimming is NA.
> Expanding genomic regions from the column center by 90 before and 90 after the center.
# A tibble: 42 x 8
   chrom start   end name           score strand center sample_name 
   <chr> <int> <int> <chr>          <dbl> <chr>   <dbl> <chr>       
 1 chr1    560   739 control_rep1|1     0 .         650 control_rep1
 2 chr1   3860  4039 control_rep1|2     0 .        3950 control_rep1
 3 chr1   4910  5089 control_rep1|4     0 .        5000 control_rep1
 4 chr1   5760  5939 control_rep1|5     0 .        5850 control_rep1
 5 chr1   6960  7139 control_rep1|6     0 .        7050 control_rep1
 6 chr10   560   739 control_rep1|7     0 .         650 control_rep1
 7 chr2    560   739 control_rep1|8     0 .         650 control_rep1
 8 chr1    110   289 control_rep2|1     0 .         200 control_rep2
 9 chr1    510   689 control_rep2|2     0 .         600 control_rep2
10 chr1   3760  3939 control_rep2|3     0 .        3850 control_rep2
# i 32 more rows
v Genomic regions were successfully centered and expanded.
  
v Genomic regions were successfully centered and expanded.
  
i Output format is set to "tibble".
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "90".
i Genomic regions will be expanded by 90bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Starting with expanding genomic regions from the column center.
> Genomic regions will be centered and expanded.
i Used genome for trimming is NA.
> Expanding genomic regions from the column center by 90 before and 90 after the center.
# A tibble: 42 x 8
   chrom start   end name           score strand center sample_name 
   <chr> <int> <int> <chr>          <dbl> <chr>   <dbl> <chr>       
 1 chr1    560   739 control_rep1|1     0 .         650 control_rep1
 2 chr1   3860  4039 control_rep1|2     0 .        3950 control_rep1
 3 chr1   4910  5089 control_rep1|4     0 .        5000 control_rep1
 4 chr1   5760  5939 control_rep1|5     0 .        5850 control_rep1
 5 chr1   6960  7139 control_rep1|6     0 .        7050 control_rep1
 6 chr10   560   739 control_rep1|7     0 .         650 control_rep1
 7 chr2    560   739 control_rep1|8     0 .         650 control_rep1
 8 chr1    110   289 control_rep2|1     0 .         200 control_rep2
 9 chr1    510   689 control_rep2|2     0 .         600 control_rep2
10 chr1   3760  3939 control_rep2|3     0 .        3850 control_rep2
# i 32 more rows
v Genomic regions were successfully centered and expanded.
  
v Genomic regions were successfully centered and expanded.
  
i Output format is set to "tibble".
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "90".
i Genomic regions will be expanded by 90bp in both direction.
  
i Argument `outputFormat` is set to "tibble".
i Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
i Argument `genome` set to NA.
i Only start will be trimmed.
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `trim_start` is FALSE.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Starting with expanding genomic regions from the column center.
> Genomic regions will be centered and expanded.
i Used genome for trimming is NA.
> Expanding genomic regions from the column center by 90 before and 90 after the center.
# A tibble: 42 x 8
   chrom start   end name           score strand center sample_name 
   <chr> <int> <int> <chr>          <dbl> <chr>   <dbl> <chr>       
 1 chr1    560   739 control_rep1|1     0 .         650 control_rep1
 2 chr1   3860  4039 control_rep1|2     0 .        3950 control_rep1
 3 chr1   4910  5089 control_rep1|4     0 .        5000 control_rep1
 4 chr1   5760  5939 control_rep1|5     0 .        5850 control_rep1
 5 chr1   6960  7139 control_rep1|6     0 .        7050 control_rep1
 6 chr10   560   739 control_rep1|7     0 .         650 control_rep1
 7 chr2    560   739 control_rep1|8     0 .         650 control_rep1
 8 chr1    110   289 control_rep2|1     0 .         200 control_rep2
 9 chr1    510   689 control_rep2|2     0 .         600 control_rep2
10 chr1   3760  3939 control_rep2|3     0 .        3850 control_rep2
# i 32 more rows
v Genomic regions were successfully centered and expanded.
  
v Genomic regions were successfully centered and expanded.
  
i Output format is set to "tibble".
# A tibble: 8 x 8
  chrom start   end name       score strand center sample_name
  <chr> <int> <int> <chr>      <dbl> <chr>   <dbl> <chr>      
1 chr1    496   699 combined|1     0 .         600 combined   
2 chr1   2796  2999 combined|2     0 .        2900 combined   
3 chr1   3846  4049 combined|3     0 .        3950 combined   
4 chr1   4771  4974 combined|4     0 .        4900 combined   
5 chr1   5946  6149 combined|5     0 .        6050 combined   
6 chr1   6946  7149 combined|6     0 .        7050 combined   
7 chr2    471   674 combined|7     0 .         550 combined   
8 chr10   471   674 combined|8     0 .         550 combined   
# A tibble: 8 x 8
  chrom start   end name       score strand center sample_name
  <chr> <int> <int> <chr>      <dbl> <chr>   <dbl> <chr>      
1 chr1    496   699 combined|1     0 .         600 combined   
2 chr1   2796  2999 combined|2     0 .        2900 combined   
3 chr1   3846  4049 combined|3     0 .        3950 combined   
4 chr1   4771  4974 combined|4     0 .        4900 combined   
5 chr1   5946  6149 combined|5     0 .        6050 combined   
6 chr1   6946  7149 combined|6     0 .        7050 combined   
7 chr2    471   674 combined|7     0 .         550 combined   
8 chr10   471   674 combined|8     0 .         550 combined   
# A tibble: 42 x 8
   chrom start   end name           score strand center sample_name 
   <chr> <int> <int> <chr>          <dbl> <chr>   <dbl> <chr>       
 1 chr1    300   999 control_rep1|1     0 .         650 control_rep1
 2 chr1   3600  4299 control_rep1|2     0 .        3950 control_rep1
 3 chr1   4650  5349 control_rep1|4     0 .        5000 control_rep1
 4 chr1   5500  6199 control_rep1|5     0 .        5850 control_rep1
 5 chr1   6700  7399 control_rep1|6     0 .        7050 control_rep1
 6 chr10   300   999 control_rep1|7     0 .         650 control_rep1
 7 chr2    300   999 control_rep1|8     0 .         650 control_rep1
 8 chr1      1   549 control_rep2|1     0 .         200 control_rep2
 9 chr1    250   949 control_rep2|2     0 .         600 control_rep2
10 chr1   3500  4199 control_rep2|3     0 .        3850 control_rep2
# i 32 more rows
ℹ Argument `outputFormat` is set to "tibble".
ℹ Argument `startsAreBased` is 1.
ℹ Argument `starts.in.df.are.0based` is FALSE.
ℹ Provide input `data` is a pre-loaded <data.frame> with the required column
  names.
→ Start preparing data.
ℹ Required columns will be added if missing.
! Column 'name' from `data` will be overwritten.
→ Column 'name' is a computed column from peakCombiner and therefore
  pre-exisiting data in a column 'name' will not be retained.
! Column 'center' does exist in `data_prepared`.
→ The column 'center' is taken to define output column 'center'.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Checking whether duplicated regions exist and need to be collapsed.
→ Checked whether duplicated regions exist and need to be collapsed.
✔ Duplicated regions identified and collapsed to unique chrom, start, and end
  for each sample by strongest score value.
  
✔ Preparation of data finished successfully.
ℹ Output format is set to "tibble".
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "350".
ℹ Genomic regions will be expanded by 350bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 350 before and 350 after
  the center.
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     251   950 control_rep1|9     80 .         601 control_rep1
 2 chr1     -49   650 control_rep1|1     96 .         301 control_rep1
 3 chr1     -49   650 control_rep1|2     95 .         301 control_rep1
 4 chr1    -149   550 control_rep1|3     46 .         201 control_rep1
 5 chr1    -249   450 control_rep1|5     26 .         101 control_rep1
 6 chr1     -49   650 control_rep1|6     25 .         301 control_rep1
 7 chr10    -49   650 control_rep1|7     75 .         301 control_rep1
 8 chr2     -49   650 control_rep1|8     50 .         301 control_rep1
 9 chr4 2   -49   650 control_rep1|10    30 .         301 control_rep1
10 chr4-2  -149   550 control_rep1|11    20 .         201 control_rep1
# ℹ 41 more rows
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites: "control_rep1|1", "control_rep1|2",
  "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7",
  "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1",
  "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5",
  "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …,
  "treatment_rep3|5", and "treatment_rep3|8".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `outputFormat` is set to "tibble".
ℹ The argument `includeByChromosomeName` is "NULL".
✔ No filtering for chromosome names in chrom is done.
  
ℹ The argument `excludeByBlacklist` is "NULL".
✔ No filtering by blacklisted regions is done.
  
ℹ The argument `includeAboveScoreCutoff` is "NULL".
✔ No filtering by score threshold is done.
  
ℹ The argument `includeTopNScoring` is "NULL".
✔ No top enriched regions were selected. All input regions are retained.
  
✔ Filtered dataset will be returned.
ℹ Output format is set to "tibble".
ℹ Argument `outputFormat` is set to "tibble".
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Start with the disjoining and filtering genomic regions.
✔ Disjoin and filter by `foundInSamples` of genomic regions successfully
  finished.
  
→ Start with combining remaining genomic regions.
✔ Combining remaining genomic regions was successfully finished.
  
→ Start with identification of overlaps between the original summit and
  remaining genomic regions.
ℹ Remaining regions without overlap will be removed.
Joining with `by = join_by(ranking)`
✔ Retained genomic regions with input data summit overlap was successfully
  finished.
  
→ Information from input center will be added to output data frame.
ℹ Argument `combinedCenter` was defined as "nearest".
ℹ The mean of all input centers is calculated and the nearest input center is
  used
→ Center information in center and score are added to the output data frame.
✔ Output data frame columns center and score were successfully populated.
  
→ No value for column sample_name was provided.
ℹ Column sample_name is filled with all input sample_names.
ℹ Column name is created as unique identifier for each row containing
  sample_name and the row number.
✔ The columns sample_name and name were successfully populated.
  
ℹ Argument `annotateWithInputNames` was set to "FALSE".
✔ Column input_names is not added to output data frame.
  
✔ All required columns in output data frame were successfully populated.
  
✔ Genomic regions were successfully combined.
  
ℹ Output format is set to "tibble".
i Argument `outputFormat` is set to "tibble".
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Start with the disjoining and filtering genomic regions.
v Disjoin and filter by `foundInSamples` of genomic regions successfully finished.
  
> Start with combining remaining genomic regions.
v Combining remaining genomic regions was successfully finished.
  
> Start with identification of overlaps between the original summit and remaining genomic regions.
i Remaining regions without overlap will be removed.
Joining with `by = join_by(ranking)`
v Retained genomic regions with input data summit overlap was successfully finished.
  
> Information from input center will be added to output data frame.
i Argument `combinedCenter` was defined as "nearest".
i The mean of all input centers is calculated and the nearest input center is used
> Center information in center and score are added to the output data frame.
v Output data frame columns center and score were successfully populated.
  
> No value for column sample_name was provided.
i Column sample_name is filled with all input sample_names.
i Column name is created as unique identifier for each row containing sample_name and the row number.
v The columns sample_name and name were successfully populated.
  
i Argument `annotateWithInputNames` was set to "FALSE".
v Column input_names is not added to output data frame.
  
v All required columns in output data frame were successfully populated.
  
v Genomic regions were successfully combined.
  
i Output format is set to "tibble".
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "350".
ℹ Genomic regions will be expanded by 350bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 350 before and 350 after
  the center.
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     251   950 control_rep1|9     80 .         601 control_rep1
 2 chr1     -49   650 control_rep1|1     96 .         301 control_rep1
 3 chr1     -49   650 control_rep1|2     95 .         301 control_rep1
 4 chr1    -149   550 control_rep1|3     46 .         201 control_rep1
 5 chr1    -249   450 control_rep1|5     26 .         101 control_rep1
 6 chr1     -49   650 control_rep1|6     25 .         301 control_rep1
 7 chr10    -49   650 control_rep1|7     75 .         301 control_rep1
 8 chr2     -49   650 control_rep1|8     50 .         301 control_rep1
 9 chr4 2   -49   650 control_rep1|10    30 .         301 control_rep1
10 chr4-2  -149   550 control_rep1|11    20 .         201 control_rep1
# ℹ 41 more rows
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites: "control_rep1|1", "control_rep1|2",
  "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7",
  "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1",
  "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5",
  "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …,
  "treatment_rep3|5", and "treatment_rep3|8".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `outputFormat` is set to "tibble".
→ The argument `includeByChromosomeName` is a class <character> of length 4 and
  will be used to retain matchhing chromsome names in chrom.
✔ Entries in chrom with the values "chr1", "chr10", "chr2", and "chr42" are
  retained.
ℹ The following 5 entries in column chrom from the input data were not
  retained: "Chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2".
✔ Input data was filtered to retain regions on defined chromosome.
  
ℹ The argument `excludeByBlacklist` is "NULL".
✔ No filtering by blacklisted regions is done.
  
ℹ The argument `includeAboveScoreCutoff` is "NULL".
✔ No filtering by score threshold is done.
  
ℹ The argument `includeTopNScoring` is "NULL".
✔ No top enriched regions were selected. All input regions are retained.
  
✔ Filtered dataset will be returned.
ℹ Output format is set to "tibble".
→ Start with the disjoining and filtering genomic regions.
✔ Disjoin and filter by `foundInSamples` of genomic regions successfully
  finished.
  
→ Start with combining remaining genomic regions.
✔ Combining remaining genomic regions was successfully finished.
  
→ Start with identification of overlaps between the original summit and
  remaining genomic regions.
ℹ Remaining regions without overlap will be removed.
Joining with `by = join_by(ranking)`
✔ Retained genomic regions with input data summit overlap was successfully
  finished.
  
→ Information from input center will be added to output data frame.
ℹ Argument `combinedCenter` was defined as "nearest".
ℹ The mean of all input centers is calculated and the nearest input center is
  used
→ Center information in center and score are added to the output data frame.
✔ Output data frame columns center and score were successfully populated.
  
→ The value "combined" for column sample_name was provided.
ℹ Column sample_name is filled with provided value combined.
ℹ Column name is created as unique identifier for each row containing
  sample_name and the row number.
✔ The columns sample_name and name were successfully populated.
  
ℹ Argument `annotateWithInputNames` was set to "TRUE".
→ Column input_names is added to output data frame.
✔ Additional column input_names was successfully populated.
  
✔ All required columns in output data frame were successfully populated.
  
> Information from input center will be added to output data frame.
i Argument `combinedCenter` was defined as "strongest".
i Based on column score the strongest input center is idenfied.
> Center information in center and score are added to the output data frame.
v Output data frame columns center and score were successfully populated.
  
> No value for column sample_name was provided.
i Column sample_name is filled with all input sample_names.
i Column name is created as unique identifier for each row containing sample_name and the row number.
v The columns sample_name and name were successfully populated.
  
i Argument `annotateWithInputNames` was set to "FALSE".
v Column input_names is not added to output data frame.
  
v All required columns in output data frame were successfully populated.
  
> Information from input center will be added to output data frame.
i Argument `combinedCenter` was defined as "middle".
i The middle between start and end and the mean score is calculated.
> Newly calculated center information are added to center and score in the output data frame.
v Output data frame columns center and score were successfully populated.
  
> No value for column sample_name was provided.
i Column sample_name is filled with all input sample_names.
i Column name is created as unique identifier for each row containing sample_name and the row number.
v The columns sample_name and name were successfully populated.
  
i Argument `annotateWithInputNames` was set to "FALSE".
v Column input_names is not added to output data frame.
  
v All required columns in output data frame were successfully populated.
  
> Information from input center will be added to output data frame.
i Argument `combinedCenter` was defined as "nearest".
i The mean of all input centers is calculated and the nearest input center is used
> Center information in center and score are added to the output data frame.
v Output data frame columns center and score were successfully populated.
  
> No value for column sample_name was provided.
i Column sample_name is filled with all input sample_names.
i Column name is created as unique identifier for each row containing sample_name and the row number.
v The columns sample_name and name were successfully populated.
  
i Argument `annotateWithInputNames` was set to "FALSE".
v Column input_names is not added to output data frame.
  
v All required columns in output data frame were successfully populated.
  
> Information from input center will be added to output data frame.
i Argument `combinedCenter` was defined as "strongest".
i Based on column score the strongest input center is idenfied.
> Center information in center and score are added to the output data frame.
v Output data frame columns center and score were successfully populated.
  
> No value for column sample_name was provided.
i Column sample_name is filled with all input sample_names.
i Column name is created as unique identifier for each row containing sample_name and the row number.
v The columns sample_name and name were successfully populated.
  
i Argument `annotateWithInputNames` was set to "FALSE".
v Column input_names is not added to output data frame.
  
v All required columns in output data frame were successfully populated.
  
> Information from input center will be added to output data frame.
i Argument `combinedCenter` was defined as "middle".
i The middle between start and end and the mean score is calculated.
> Newly calculated center information are added to center and score in the output data frame.
v Output data frame columns center and score were successfully populated.
  
> No value for column sample_name was provided.
i Column sample_name is filled with all input sample_names.
i Column name is created as unique identifier for each row containing sample_name and the row number.
v The columns sample_name and name were successfully populated.
  
i Argument `annotateWithInputNames` was set to "FALSE".
v Column input_names is not added to output data frame.
  
v All required columns in output data frame were successfully populated.
  
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "350".
ℹ Genomic regions will be expanded by 350bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 350 before and 350 after
  the center.
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     251   950 control_rep1|9     80 .         601 control_rep1
 2 chr1     -49   650 control_rep1|1     96 .         301 control_rep1
 3 chr1     -49   650 control_rep1|2     95 .         301 control_rep1
 4 chr1    -149   550 control_rep1|3     46 .         201 control_rep1
 5 chr1    -249   450 control_rep1|5     26 .         101 control_rep1
 6 chr1     -49   650 control_rep1|6     25 .         301 control_rep1
 7 chr10    -49   650 control_rep1|7     75 .         301 control_rep1
 8 chr2     -49   650 control_rep1|8     50 .         301 control_rep1
 9 chr4 2   -49   650 control_rep1|10    30 .         301 control_rep1
10 chr4-2  -149   550 control_rep1|11    20 .         201 control_rep1
# ℹ 41 more rows
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites: "control_rep1|1", "control_rep1|2",
  "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7",
  "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1",
  "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5",
  "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …,
  "treatment_rep3|5", and "treatment_rep3|8".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `outputFormat` is set to "tibble".
ℹ The argument `includeByChromosomeName` is "NULL".
✔ No filtering for chromosome names in chrom is done.
  
ℹ The argument `excludeByBlacklist` is "NULL".
✔ No filtering by blacklisted regions is done.
  
ℹ The argument `includeAboveScoreCutoff` is "NULL".
✔ No filtering by score threshold is done.
  
ℹ The argument `includeTopNScoring` is "NULL".
✔ No top enriched regions were selected. All input regions are retained.
  
✔ Filtered dataset will be returned.
ℹ Output format is set to "tibble".
→ Start with the disjoining and filtering genomic regions.
✔ Disjoin and filter by `foundInSamples` of genomic regions successfully
  finished.
  
> Start with the disjoining and filtering genomic regions.
v Disjoin and filter by `foundInSamples` of genomic regions successfully finished.
  
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "350".
ℹ Genomic regions will be expanded by 350bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 350 before and 350 after
  the center.
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     251   950 control_rep1|9     80 .         601 control_rep1
 2 chr1     -49   650 control_rep1|1     96 .         301 control_rep1
 3 chr1     -49   650 control_rep1|2     95 .         301 control_rep1
 4 chr1    -149   550 control_rep1|3     46 .         201 control_rep1
 5 chr1    -249   450 control_rep1|5     26 .         101 control_rep1
 6 chr1     -49   650 control_rep1|6     25 .         301 control_rep1
 7 chr10    -49   650 control_rep1|7     75 .         301 control_rep1
 8 chr2     -49   650 control_rep1|8     50 .         301 control_rep1
 9 chr4 2   -49   650 control_rep1|10    30 .         301 control_rep1
10 chr4-2  -149   550 control_rep1|11    20 .         201 control_rep1
# ℹ 41 more rows
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites: "control_rep1|1", "control_rep1|2",
  "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7",
  "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1",
  "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5",
  "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …,
  "treatment_rep3|5", and "treatment_rep3|8".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `outputFormat` is set to "tibble".
→ The argument `includeByChromosomeName` is a class <character> of length 4 and
  will be used to retain matchhing chromsome names in chrom.
✔ Entries in chrom with the values "chr1", "chr10", "chr2", and "chr42" are
  retained.
ℹ The following 5 entries in column chrom from the input data were not
  retained: "Chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2".
✔ Input data was filtered to retain regions on defined chromosome.
  
ℹ The argument `excludeByBlacklist` is "NULL".
✔ No filtering by blacklisted regions is done.
  
ℹ The argument `includeAboveScoreCutoff` is "NULL".
✔ No filtering by score threshold is done.
  
ℹ The argument `includeTopNScoring` is "NULL".
✔ No top enriched regions were selected. All input regions are retained.
  
✔ Filtered dataset will be returned.
ℹ Output format is set to "tibble".
→ Start with the disjoining and filtering genomic regions.
✔ Disjoin and filter by `foundInSamples` of genomic regions successfully
  finished.
  
→ Start with combining remaining genomic regions.
✔ Combining remaining genomic regions was successfully finished.
  
→ Start with identification of overlaps between the original summit and
  remaining genomic regions.
ℹ Remaining regions without overlap will be removed.
Joining with `by = join_by(ranking)`
✔ Retained genomic regions with input data summit overlap was successfully
  finished.
  
→ Start with identification of overlaps between the original summit and
  remaining genomic regions.
ℹ Remaining regions without overlap will be removed.
Joining with `by = join_by(ranking)`
✔ Retained genomic regions with input data summit overlap was successfully
  finished.
  
ℹ Regions are not checked for overlap with innput summits.  Nothing is removed.
✔ Retained genomic regions with input data summit overlap was successfully
  finished.
  
ℹ Regions are not checked for overlap with innput summits.  Nothing is removed.
✔ Retained genomic regions with input data summit overlap was successfully
  finished.
  
→ Start with identification of overlaps between the original summit and
  remaining genomic regions.
ℹ Remaining regions without overlap will be removed.
Joining with `by = join_by(ranking)`
✔ Retained genomic regions with input data summit overlap was successfully
  finished.
  
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "350".
ℹ Genomic regions will be expanded by 350bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 350 before and 350 after
  the center.
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     251   950 control_rep1|9     80 .         601 control_rep1
 2 chr1     -49   650 control_rep1|1     96 .         301 control_rep1
 3 chr1     -49   650 control_rep1|2     95 .         301 control_rep1
 4 chr1    -149   550 control_rep1|3     46 .         201 control_rep1
 5 chr1    -249   450 control_rep1|5     26 .         101 control_rep1
 6 chr1     -49   650 control_rep1|6     25 .         301 control_rep1
 7 chr10    -49   650 control_rep1|7     75 .         301 control_rep1
 8 chr2     -49   650 control_rep1|8     50 .         301 control_rep1
 9 chr4 2   -49   650 control_rep1|10    30 .         301 control_rep1
10 chr4-2  -149   550 control_rep1|11    20 .         201 control_rep1
# ℹ 41 more rows
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites: "control_rep1|1", "control_rep1|2",
  "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7",
  "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1",
  "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5",
  "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …,
  "treatment_rep3|5", and "treatment_rep3|8".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `outputFormat` is set to "tibble".
→ The argument `includeByChromosomeName` is a class <character> of length 4 and
  will be used to retain matchhing chromsome names in chrom.
✔ Entries in chrom with the values "chr1", "chr10", "chr2", and "chr42" are
  retained.
ℹ The following 5 entries in column chrom from the input data were not
  retained: "Chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2".
✔ Input data was filtered to retain regions on defined chromosome.
  
ℹ The argument `excludeByBlacklist` is "NULL".
✔ No filtering by blacklisted regions is done.
  
ℹ The argument `includeAboveScoreCutoff` is "NULL".
✔ No filtering by score threshold is done.
  
ℹ The argument `includeTopNScoring` is "NULL".
✔ No top enriched regions were selected. All input regions are retained.
  
✔ Filtered dataset will be returned.
ℹ Output format is set to "tibble".
→ Start with the disjoining and filtering genomic regions.
✔ Disjoin and filter by `foundInSamples` of genomic regions successfully
  finished.
  
→ Start with combining remaining genomic regions.
✔ Combining remaining genomic regions was successfully finished.
  
i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion.
v `expandBy` was calculated from the input data and set to "350".
i Genomic regions will be expanded by 350bp in both direction.
  
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "350".
ℹ Genomic regions will be expanded by 350bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 350 before and 350 after
  the center.
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     251   950 control_rep1|9     80 .         601 control_rep1
 2 chr1     -49   650 control_rep1|1     96 .         301 control_rep1
 3 chr1     -49   650 control_rep1|2     95 .         301 control_rep1
 4 chr1    -149   550 control_rep1|3     46 .         201 control_rep1
 5 chr1    -249   450 control_rep1|5     26 .         101 control_rep1
 6 chr1     -49   650 control_rep1|6     25 .         301 control_rep1
 7 chr10    -49   650 control_rep1|7     75 .         301 control_rep1
 8 chr2     -49   650 control_rep1|8     50 .         301 control_rep1
 9 chr4 2   -49   650 control_rep1|10    30 .         301 control_rep1
10 chr4-2  -149   550 control_rep1|11    20 .         201 control_rep1
# ℹ 41 more rows
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites: "control_rep1|1", "control_rep1|2",
  "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7",
  "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1",
  "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5",
  "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …,
  "treatment_rep3|5", and "treatment_rep3|8".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `outputFormat` is set to "tibble".
ℹ The argument `includeByChromosomeName` is "NULL".
✔ No filtering for chromosome names in chrom is done.
  
ℹ The argument `excludeByBlacklist` is "NULL".
✔ No filtering by blacklisted regions is done.
  
ℹ The argument `includeAboveScoreCutoff` is "NULL".
✔ No filtering by score threshold is done.
  
ℹ The argument `includeTopNScoring` is "NULL".
✔ No top enriched regions were selected. All input regions are retained.
  
✔ Filtered dataset will be returned.
ℹ Output format is set to "tibble".
ℹ Argument `outputFormat` is set to "tibble".
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Start with the disjoining and filtering genomic regions.
✔ Disjoin and filter by `foundInSamples` of genomic regions successfully
  finished.
  
→ Start with combining remaining genomic regions.
✔ Combining remaining genomic regions was successfully finished.
  
→ Start with identification of overlaps between the original summit and
  remaining genomic regions.
ℹ Remaining regions without overlap will be removed.
Joining with `by = join_by(ranking)`
✔ Retained genomic regions with input data summit overlap was successfully
  finished.
  
→ Information from input center will be added to output data frame.
ℹ Argument `combinedCenter` was defined as "nearest".
ℹ The mean of all input centers is calculated and the nearest input center is
  used
→ Center information in center and score are added to the output data frame.
✔ Output data frame columns center and score were successfully populated.
  
→ No value for column sample_name was provided.
ℹ Column sample_name is filled with all input sample_names.
ℹ Column name is created as unique identifier for each row containing
  sample_name and the row number.
✔ The columns sample_name and name were successfully populated.
  
ℹ Argument `annotateWithInputNames` was set to "FALSE".
✔ Column input_names is not added to output data frame.
  
✔ All required columns in output data frame were successfully populated.
  
✔ Genomic regions were successfully combined.
  
ℹ Output format is set to "tibble".
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "324".
ℹ Genomic regions will be expanded by 324bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 324 before and 324 after
  the center.
# A tibble: 5 × 8
  chrom  start   end name                        score strand center sample_name
  <chr>  <int> <int> <chr>                       <dbl> <chr>   <dbl> <chr>      
1 chr1     -23   624 control_rep1|control_rep2|…   100 .         301 control_re…
2 chr2     -23   624 control_rep1|control_rep2|…    50 .         301 control_re…
3 chr10    -23   624 control_rep1|control_rep2|…    95 .         301 control_re…
4 chr4 2   -23   624 control_rep1|control_rep2|…    35 .         301 control_re…
5 chr4-2   -23   624 control_rep1|control_rep2|…    30 .         301 control_re…
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites:
  "control_rep1|control_rep2|control_rep3|treatment_rep1|treatment_rep2|treatment_rep3|1",
  "control_rep1|control_rep2|control_rep3|treatment_rep1|treatment_rep2|treatment_rep3|2",
  "control_rep1|control_rep2|control_rep3|treatment_rep1|treatment_rep2|treatment_rep3|3",
  "control_rep1|control_rep2|control_rep3|treatment_rep1|treatment_rep2|treatment_rep3|4",
  and
  "control_rep1|control_rep2|control_rep3|treatment_rep1|treatment_rep2|treatment_rep3|5".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `outputFormat` is set to "tibble".
i The argument `includeByChromosomeName` is "NULL".
v No filtering for chromosome names in chrom is done.
  
i The argument `excludeByBlacklist` is "NULL".
v No filtering by blacklisted regions is done.
  
i The argument `includeAboveScoreCutoff` is "NULL".
v No filtering by score threshold is done.
  
i The argument `includeTopNScoring` is "NULL".
v No top enriched regions were selected. All input regions are retained.
  
v Filtered dataset will be returned.
i Output format is set to "tibble".
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `outputFormat` is set to "tibble".
i The argument `includeByChromosomeName` is "NULL".
v No filtering for chromosome names in chrom is done.
  
i The argument `excludeByBlacklist` is "NULL".
v No filtering by blacklisted regions is done.
  
i The argument `includeAboveScoreCutoff` is "NULL".
v No filtering by score threshold is done.
  
i The argument `includeTopNScoring` is "NULL".
v No top enriched regions were selected. All input regions are retained.
  
v Filtered dataset will be returned.
i Output format is set to "tibble".
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `outputFormat` is set to "tibble".
i The argument `includeByChromosomeName` is "NULL".
v No filtering for chromosome names in chrom is done.
  
i The argument `excludeByBlacklist` is "NULL".
v No filtering by blacklisted regions is done.
  
i The argument `includeAboveScoreCutoff` is "NULL".
v No filtering by score threshold is done.
  
i The argument `includeTopNScoring` is "NULL".
v No top enriched regions were selected. All input regions are retained.
  
v Filtered dataset will be returned.
i Output format is set to "tibble".
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `outputFormat` is set to "tibble".
i The argument `includeByChromosomeName` is "NULL".
v No filtering for chromosome names in chrom is done.
  
i The argument `excludeByBlacklist` is "NULL".
v No filtering by blacklisted regions is done.
  
i The argument `includeAboveScoreCutoff` is "NULL".
v No filtering by score threshold is done.
  
i The argument `includeTopNScoring` is "NULL".
v No top enriched regions were selected. All input regions are retained.
  
v Filtered dataset will be returned.
i Output format is set to "tibble".
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `outputFormat` is set to "tibble".
i The argument `includeByChromosomeName` is "NULL".
v No filtering for chromosome names in chrom is done.
  
i The argument `excludeByBlacklist` is "NULL".
v No filtering by blacklisted regions is done.
  
i The argument `includeAboveScoreCutoff` is "NULL".
v No filtering by score threshold is done.
  
i The argument `includeTopNScoring` is "NULL".
v No top enriched regions were selected. All input regions are retained.
  
v Filtered dataset will be returned.
i Output format is set to "tibble".
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
i Provide input `data` is a <data.frame> with three or four columns and paths to existing files.
> Start loading and preparing data.
i Argument `outputFormat` is set to "tibble".
i The argument `includeByChromosomeName` is "NULL".
v No filtering for chromosome names in chrom is done.
  
i The argument `excludeByBlacklist` is "NULL".
v No filtering by blacklisted regions is done.
  
i The argument `includeAboveScoreCutoff` is "NULL".
v No filtering by score threshold is done.
  
i The argument `includeTopNScoring` is "NULL".
v No top enriched regions were selected. All input regions are retained.
  
v Filtered dataset will be returned.
i Output format is set to "tibble".
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "350".
ℹ Genomic regions will be expanded by 350bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 350 before and 350 after
  the center.
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     251   950 control_rep1|9     80 .         601 control_rep1
 2 chr1     -49   650 control_rep1|1     96 .         301 control_rep1
 3 chr1     -49   650 control_rep1|2     95 .         301 control_rep1
 4 chr1    -149   550 control_rep1|3     46 .         201 control_rep1
 5 chr1    -249   450 control_rep1|5     26 .         101 control_rep1
 6 chr1     -49   650 control_rep1|6     25 .         301 control_rep1
 7 chr10    -49   650 control_rep1|7     75 .         301 control_rep1
 8 chr2     -49   650 control_rep1|8     50 .         301 control_rep1
 9 chr4 2   -49   650 control_rep1|10    30 .         301 control_rep1
10 chr4-2  -149   550 control_rep1|11    20 .         201 control_rep1
# ℹ 41 more rows
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites: "control_rep1|1", "control_rep1|2",
  "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7",
  "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1",
  "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5",
  "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …,
  "treatment_rep3|5", and "treatment_rep3|8".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
→ The argument `includeByChromosomeName` is a class <character> of length 3 and
  will be used to retain matchhing chromsome names in chrom.
✔ Entries in chrom with the values "chr1", "chr10", and "chr42" are retained.
ℹ The following 6 entries in column chrom from the input data were not
  retained: "Chr2", "chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2".
✔ Input data was filtered to retain regions on defined chromosome.
  
→ User provied dataframe will be used for blacklist filtering.
! Provided blacklist contains chromosome names (in chrom) not found in input
  data.
ℹ The following blacklist chromosomes have no match: "chr1" and "chr42".
→ Note to user: Please doublecheck this observation.
✔ Input data was filtered by blacklist.
  
> User provied dataframe will be used for blacklist filtering.
! Provided blacklist contains chromosome names (in chrom) not found in input data.
i The following blacklist chromosomes have no match: "chr1" and "chr42".
> Note to user: Please doublecheck this observation.
v Input data was filtered by blacklist.
  
i The argument `excludeByBlacklist` is "NULL".
v No filtering by blacklisted regions is done.
  
i The argument `excludeByBlacklist` is "NULL".
v No filtering by blacklisted regions is done.
  
> User provied GenomicRanges object will be used for blacklist filtering.
! Provided blacklist contains chromosome names (in chrom) not found in input data.
i The following blacklist chromosomes have no match: "chr1" and "chr42".
> Note to user: Please doublecheck this observation.
i The argument `excludeByBlacklist` is a class <GRanges>.
> Using GenmoicRanges option for filtering.
v Input data was filtered by blacklist.
  
> User provied dataframe will be used for blacklist filtering.
! Provided blacklist contains chromosome names (in chrom) not found in input data.
i The following blacklist chromosomes have no match: "chr1" and "chr42".
> Note to user: Please doublecheck this observation.
v Input data was filtered by blacklist.
  
> User provied dataframe will be used for blacklist filtering.
! Provided blacklist contains chromosome names (in chrom) not found in input data.
i The following blacklist chromosomes have no match: "chr1" and "chr42".
> Note to user: Please doublecheck this observation.
v Input data was filtered by blacklist.
  
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "350".
ℹ Genomic regions will be expanded by 350bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 350 before and 350 after
  the center.
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     251   950 control_rep1|9     80 .         601 control_rep1
 2 chr1     -49   650 control_rep1|1     96 .         301 control_rep1
 3 chr1     -49   650 control_rep1|2     95 .         301 control_rep1
 4 chr1    -149   550 control_rep1|3     46 .         201 control_rep1
 5 chr1    -249   450 control_rep1|5     26 .         101 control_rep1
 6 chr1     -49   650 control_rep1|6     25 .         301 control_rep1
 7 chr10    -49   650 control_rep1|7     75 .         301 control_rep1
 8 chr2     -49   650 control_rep1|8     50 .         301 control_rep1
 9 chr4 2   -49   650 control_rep1|10    30 .         301 control_rep1
10 chr4-2  -149   550 control_rep1|11    20 .         201 control_rep1
# ℹ 41 more rows
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites: "control_rep1|1", "control_rep1|2",
  "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7",
  "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1",
  "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5",
  "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …,
  "treatment_rep3|5", and "treatment_rep3|8".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
→ The argument `includeByChromosomeName` is a class <character> of length 3 and
  will be used to retain matchhing chromsome names in chrom.
✔ Entries in chrom with the values "chr1", "chr10", and "chr42" are retained.
ℹ The following 6 entries in column chrom from the input data were not
  retained: "Chr2", "chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2".
✔ Input data was filtered to retain regions on defined chromosome.
  
> The argument `includeByChromosomeName` is a class <character> of length 3 and will be used to retain matchhing chromsome names in chrom.
v Entries in chrom with the values "chr1", "chr10", and "chr42" are retained.
i The following 6 entries in column chrom from the input data were not retained: "Chr2", "chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2".
v Input data was filtered to retain regions on defined chromosome.
  
i The argument `includeByChromosomeName` is "NULL".
v No filtering for chromosome names in chrom is done.
  
> The argument `includeByChromosomeName` is a class <character> of length 1 and will be used to retain matchhing chromsome names in chrom.
v Entries in chrom with the value "chr1" are retained.
i The following 2 entries in column chrom from the input data were not retained: "chr10" and "chr42".
v Input data was filtered to retain regions on defined chromosome.
  
> The argument `includeByChromosomeName` is a class <character> of length 3 and will be used to retain matchhing chromsome names in chrom.
v Entries in chrom with the values "chr1", "chr10", and "chr42" are retained.
v Input data was filtered to retain regions on defined chromosome.
  
! `includeByChromosomeName` has the wrong class.
> `includeByChromosomeName` is converted to <character>.
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "350".
ℹ Genomic regions will be expanded by 350bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 350 before and 350 after
  the center.
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     251   950 control_rep1|9     80 .         601 control_rep1
 2 chr1     -49   650 control_rep1|1     96 .         301 control_rep1
 3 chr1     -49   650 control_rep1|2     95 .         301 control_rep1
 4 chr1    -149   550 control_rep1|3     46 .         201 control_rep1
 5 chr1    -249   450 control_rep1|5     26 .         101 control_rep1
 6 chr1     -49   650 control_rep1|6     25 .         301 control_rep1
 7 chr10    -49   650 control_rep1|7     75 .         301 control_rep1
 8 chr2     -49   650 control_rep1|8     50 .         301 control_rep1
 9 chr4 2   -49   650 control_rep1|10    30 .         301 control_rep1
10 chr4-2  -149   550 control_rep1|11    20 .         201 control_rep1
# ℹ 41 more rows
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites: "control_rep1|1", "control_rep1|2",
  "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7",
  "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1",
  "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5",
  "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …,
  "treatment_rep3|5", and "treatment_rep3|8".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
→ Significance in score is filtered and all regions above 40 will be retained.
ℹ A total of 37 of 51 input regions are retained with value in score a above
  40.
✔ Input data was filtered to retain regions with a score above the defined
  threshold.
  
> Significance in score is filtered and all regions above 0.01 will be retained.
i A total of 51 of 51 input regions are retained with value in score a above 0.01.
v Input data was filtered to retain regions with a score above the defined threshold.
  
i The argument `includeAboveScoreCutoff` is "NULL".
v No filtering by score threshold is done.
  
> Significance in score is filtered and all regions above 0 will be retained.
i A total of 37 of 37 input regions are retained with value in score a above 0.
v Input data was filtered to retain regions with a score above the defined threshold.
  
ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is
  calculated and returned for expansion.
✔ `expandBy` was calculated from the input data and set to "350".
ℹ Genomic regions will be expanded by 350bp in both direction.
  
ℹ Argument `outputFormat` is set to "tibble".
ℹ Input data `data` has no assigned genome.
! Input data `data` has no assigned genome (NA).
ℹ Argument `genome` set to NA.
ℹ Only start will be trimmed.
ℹ Provide input `data` is a <data.frame> with three or four columns and paths
  to existing files.
→ Start loading and preparing data.
ℹ Argument `trim_start` is TRUE.
→ Checking <class> and "values" of all columns.
✔ Structure of data was successfully checked to be an accepted input.
  
→ Starting with expanding genomic regions from the column center.
→ Genomic regions will be centered and expanded.
ℹ Used genome for trimming is NA.
→ Expanding genomic regions from the column center by 350 before and 350 after
  the center.
# A tibble: 51 × 8
   chrom  start   end name            score strand center sample_name 
   <chr>  <int> <int> <chr>           <dbl> <chr>   <dbl> <chr>       
 1 Chr2     251   950 control_rep1|9     80 .         601 control_rep1
 2 chr1     -49   650 control_rep1|1     96 .         301 control_rep1
 3 chr1     -49   650 control_rep1|2     95 .         301 control_rep1
 4 chr1    -149   550 control_rep1|3     46 .         201 control_rep1
 5 chr1    -249   450 control_rep1|5     26 .         101 control_rep1
 6 chr1     -49   650 control_rep1|6     25 .         301 control_rep1
 7 chr10    -49   650 control_rep1|7     75 .         301 control_rep1
 8 chr2     -49   650 control_rep1|8     50 .         301 control_rep1
 9 chr4 2   -49   650 control_rep1|10    30 .         301 control_rep1
10 chr4-2  -149   550 control_rep1|11    20 .         201 control_rep1
# ℹ 41 more rows
✔ Genomic regions were successfully centered and expanded.
  
ℹ Argument `trim_start` is set to "TRUE".
ℹ Atgument `genome` is set to NA.
→ Trimming start coordinates of resulting genomic regions.
ℹ Some newly-defined genomic regions have a start coordinate below "1".
→ Values of name for these sites: "control_rep1|1", "control_rep1|2",
  "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7",
  "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1",
  "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5",
  "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …,
  "treatment_rep3|5", and "treatment_rep3|8".
✔ These genomic regions were trimmed to get start coordinate "1".
✔ Genomic regions were successfully centered and expanded.
  
ℹ Output format is set to "tibble".
ℹ The argument `includeTopNScoring` extracted the the top 10 regions by score
  per sample (based on the values in sample_name).
→ The top enriched 10 regions per sample will be retained.
ℹ The argument `includeTopNScoring` was defined as 10.
→ The following "sample_names" contain less regions then defined by
  `includeTopNScoring`: control_rep2, control_rep3, treatment_rep1,
  treatment_rep2, and treatment_rep3
! No genomic regions will be removed for such samples.
✔ Input data was filtered and the top 10 enriched regions per sample are
  retained.
  
i The argument `includeTopNScoring` extracted the the top 10 regions by score per sample (based on the values in sample_name).
> The top enriched 10 regions per sample will be retained.
i The argument `includeTopNScoring` was defined as 10.
> The following "sample_names" contain less regions then defined by `includeTopNScoring`: control_rep2, control_rep3, treatment_rep1, treatment_rep2, and treatment_rep3
! No genomic regions will be removed for such samples.
v Input data was filtered and the top 10 enriched regions per sample are retained.
  
i The argument `includeTopNScoring` is "NULL".
v No top enriched regions were selected. All input regions are retained.
  
i The argument `includeTopNScoring` extracted the the top 5 regions by score per sample (based on the values in sample_name).
> The top enriched 5 regions per sample will be retained.
v Input data was filtered and the top 5 enriched regions per sample are retained.
  
i Argument `outputFormat` is set to "GenomicRanges".
i Argument `startsAreBased` is 1.
i Argument `starts.in.df.are.0based` is FALSE.
i Provide input `data` is a pre-loaded <data.frame> with the required column names.
> Start preparing data.
i Required columns will be added if missing.
! Column 'name' from `data` will be overwritten.
> Column 'name' is a computed column from peakCombiner and therefore pre-exisiting data in a column 'name' will not be retained.
! Column 'center' does exist in `data_prepared`.
> The column 'center' is taken to define output column 'center'.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
> Checking whether duplicated regions exist and need to be collapsed.
> Checked whether duplicated regions exist and need to be collapsed.
v Duplicated regions identified and collapsed to unique chrom, start, and end for each sample by strongest score value.
  
v Preparation of data finished successfully.
i Output format is set to "GenomicRanges".
i No input genome annotation assigned to ouutput.
> Checking <class> and "values" of all columns.
v Structure of data was successfully checked to be an accepted input.
  
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 479 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 479 ]
> 
> proc.time()
   user  system elapsed 
 53.358   1.488  55.519