##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings EpiCompare_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/EpiCompare.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘EpiCompare/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EpiCompare’ version ‘1.13.1’
* 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 ‘EpiCompare’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) EpiCompare.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:76-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:82-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:84-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:181: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:183: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_consensus_peaks.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_consensus_peaks.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_corr.Rd:62-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_corr.Rd:66-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_corr.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files_names.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files_names.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files_names.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files_names.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gather_files_names.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liftover_grlist.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liftover_grlist.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) overlap_stat_plot.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overlap_stat_plot.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_corr.Rd:64-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_corr.Rd:68-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_corr.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_precision_recall.Rd:47-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_precision_recall.Rd:51-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_precision_recall.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) precision_recall.Rd:42-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) precision_recall.Rd:46-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) precision_recall.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:13-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_peaks.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_peaks.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_peaks.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_peaks.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_peaks.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rebin_peaks.Rd:39-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rebin_peaks.Rd:43-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rebin_peaks.Rd:47-49: Lost braces in \itemize; meant \describe ?
* 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 ... ERROR
Running examples in ‘EpiCompare-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_precision_recall
> ### Title: Plot precision-recall curves
> ### Aliases: plot_precision_recall
> 
> ### ** Examples
> 
> data("CnR_H3K27ac")
> data("CnT_H3K27ac")
> data("encode_H3K27ac")
> peakfiles <- list(CnR_H3K27ac=CnR_H3K27ac, CnT_H3K27ac=CnT_H3K27ac)
> reference <- list("encode_H3K27ac" = encode_H3K27ac)
> 
> pr_out <- plot_precision_recall(peakfiles = peakfiles,
+                                 reference = reference,
+                                 workers = 1)
Threshold=0: Filtering peaks
Threshold=0.05: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.1: Filtering peaks
Threshold=0.15: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.2: Filtering peaks
Threshold=0.25: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.3: Filtering peaks
Threshold=0.35: Filtering peaks
Computing precision-recall results.
Threshold=0.4: Filtering peaks
Computing precision-recall results.
Threshold=0.45: Filtering peaks
Computing precision-recall results.
Threshold=0.5: Filtering peaks
Computing precision-recall results.
Threshold=0.55: Filtering peaks
Computing precision-recall results.
Threshold=0.6: Filtering peaks
Computing precision-recall results.
Threshold=0.65: Filtering peaks
Computing precision-recall results.
Threshold=0.7: Filtering peaks
Computing precision-recall results.
Threshold=0.75: Filtering peaks
Computing precision-recall results.
Threshold=0.8: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.85: Filtering peaks
Threshold=0.9: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.95: Filtering peaks
Computing precision-recall results.
Reformatting precision-recall data.
Saving precision-recall results ==> /tmp/RtmpIEzq8e/file2f937c4fe9caaeprecision_recall.csv
Plotting precision-recall curve.
Error:
! The `facets` argument of `facet_grid()` was deprecated in ggplot2
  2.2.0 and is now defunct.
ℹ Please use the `rows` argument instead.
Backtrace:
    ▆
 1. └─EpiCompare::plot_precision_recall(...)
 2.   └─EpiCompare:::plot_precision_recall_prcurve(...)
 3.     └─ggplot2::facet_grid(facets = facets)
 4.       └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
 5.         └─lifecycle:::deprecate_stop0(msg)
 6.           └─rlang::cnd_signal(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
plot_enrichment            42.994  1.003  52.366
plot_ChIPseeker_annotation 34.172  0.875  43.251
EpiCompare                 10.179  0.957  11.199
plot_corr                   5.468  1.131   5.185
plot_chromHMM               5.884  0.267   9.603
compute_corr                3.674  1.380   3.842
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0 and is now defunct.
  i Please use the `rows` argument instead.
  Backtrace:
      ▆
   1. └─EpiCompare::plot_precision_recall(...) at test-plot_precision_recall.R:9:5
   2.   └─EpiCompare:::plot_precision_recall_prcurve(...)
   3.     └─ggplot2::facet_grid(facets = facets)
   4.       └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
   5.         └─lifecycle:::deprecate_stop0(msg)
   6.           └─rlang::cnd_signal(...)
  
  [ FAIL 2 | WARN 5 | SKIP 0 | PASS 81 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/EpiCompare.Rcheck/00check.log’
for details.

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


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘EpiCompare’ ...
** this is package ‘EpiCompare’ version ‘1.13.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package keeps a record of temporary installation path
* DONE (EpiCompare)

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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(EpiCompare)

Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' 
> 
> test_check("EpiCompare")
All EpiCompare features are being used.
WARNING: precision-recall curves cannot be generated when reference=NULL.


processing file: EpiCompare.Rmd

Quitting from EpiCompare.Rmd:344-359 [overlap_upset_plot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Removing non-standard chromosomes.
Computing consensus peaks for group: Imperial 
 - 2 files 
 - 1,670-2,707 peaks each
Identified 1,325 consensus peaks from 2 peak files
Computing consensus peaks for group: ENCODE 
 - 1 files 
 - 5,142-5,142 peaks each
WARNING: Cannot compute consensus peaks when group has <2 peak files. Returning original GRanges object instead.
Done computing consensus peaks in 0.01 min.
Removing non-standard chromosomes.
Computing consensus peaks for group: Imperial 
 - 2 files 
 - 1,670-2,707 peaks each
Identified 2,982 consensus peaks from 2 peak files
Computing consensus peaks for group: ENCODE 
 - 1 files 
 - 5,142-5,142 peaks each
WARNING: Cannot compute consensus peaks when group has <2 peak files. Returning original GRanges object instead.
Done computing consensus peaks in 0.35 min.
Standardising peak files in 6,659 bins of 5e+05 bp.
Merging data into matrix.
Binned matrix size: 6,659 x 3
Matrix sparsity: 0.9526
Calculating correlation matrix.
Done computing correlations in 2 seconds.
Saving correlation results ==> /tmp/Rtmp73dIua/file2fcb15196e7d39.corr.csv.gz
Standardising peak files in 32,488 bins of 1e+05 bp.
Merging data into matrix.
Binned matrix size: 32,488 x 3
Matrix sparsity: 0.974
Calculating correlation matrix.
Done computing correlations in 2 seconds.
Saving correlation results ==> /tmp/Rtmp73dIua/file2fcb15c514289.corr.csv.gz
Standardising peak files in 323,636 bins of 1e+04 bp.
Merging data into matrix.
Binned matrix size: 323,636 x 3
Matrix sparsity: 0.9936
Calculating correlation matrix.
Done computing correlations in 4 seconds.
Saving correlation results ==> /tmp/Rtmp73dIua/file2fcb1550c1ee10.corr.csv.gz
Standardising peak files in 647,114 bins of 5,000 bp.
Merging data into matrix.
Binned matrix size: 647,114 x 3
Matrix sparsity: 0.996
Calculating correlation matrix.
Done computing correlations in 6 seconds.
Saving correlation results ==> /tmp/Rtmp73dIua/file2fcb1543dfdc80.corr.csv.gz
--- Running fragment_info() ---
Done.
Writing ==> /tmp/Rtmp73dIua/processed_results/encode_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/Rtmp73dIua/processed_results/CnT_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/Rtmp73dIua/processed_results/CnR_H3K27ac.narrowPeaks.bed
Searching for *.narrowPeaks.bed$ files...
3 matching files identified.
Constructing file names.
Importing files.
Reading narrowPeaks
Reading narrowPeaks
Reading narrowPeaks
3 files retrieved.
Searching for peaks.narrow files...
3 matching files identified.
Constructing file names.
Returning paths.
Searching for peaks.narrow files...
0 matching files identified. Returning NULL.
Writing ==> /tmp/Rtmp73dIua/processed_results/encode_H3K27ac.narrowPeaks.bed
Preparing chain file.
loading from cache
require("rtracklayer")
Performing liftover:  hg19  -->  hg38
Removing non-standard chromosomes.
Preparing chain file.
Preparing chain file.
loading from cache
Performing liftover:  hg38  -->  hg19
Removing non-standard chromosomes.
loading from cache
Performing liftover:  hg19  -->  mm9
Removing non-standard chromosomes.
NOTE: The following EpiCompare features are NOT being used: 
 - upset_plot=
 - stat_plot=
 - chromHMM_plot=
 - chipseeker_plot=
 - enrichment_plot=
 - tss_plot=
 - precision_recall_plot=
 - corr_plot=
 - add_download_button=


processing file: EpiCompare.Rmd
output file: EpiCompare.knit.md

/usr/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp73dIua/t1/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp73dIua/rmarkdown-str2fcb155a6530f7.html --variable code_folding=hide --variable code_menu=1 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'EpiCompare.knit'

Output created: /tmp/Rtmp73dIua/t1/EpiCompare.html
[1] "Done in 0.13 min."
All outputs saved to: /tmp/Rtmp73dIua/t1
NOTE: The following EpiCompare features are NOT being used: 
 - upset_plot=
 - stat_plot=
 - chromHMM_plot=
 - chipseeker_plot=
 - enrichment_plot=
 - tss_plot=
 - precision_recall_plot=
 - corr_plot=
 - add_download_button=


processing file: EpiCompare.Rmd
output file: EpiCompare.knit.md

/usr/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp73dIua/t2/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp73dIua/rmarkdown-str2fcb1565cb42e0.html --variable code_folding=hide --variable code_menu=1 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'EpiCompare.knit'

Output created: /tmp/Rtmp73dIua/t2/EpiCompare.html
[1] "Done in 0.14 min."
All outputs saved to: /tmp/Rtmp73dIua/t2
NOTE: The following EpiCompare features are NOT being used: 
 - upset_plot=
 - stat_plot=
 - chromHMM_plot=
 - chipseeker_plot=
 - enrichment_plot=
 - tss_plot=
 - precision_recall_plot=
 - corr_plot=
 - add_download_button=


processing file: EpiCompare.Rmd
output file: EpiCompare.knit.md

/usr/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp73dIua/t3/testthat_example_Sep_22_2025.html --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp73dIua/rmarkdown-str2fcb1567df10b0.html --variable code_folding=hide --variable code_menu=1 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'EpiCompare.knit'

Output created: /tmp/Rtmp73dIua/t3/testthat_example_Sep_22_2025.html
[1] "Done in 0.13 min."
All outputs saved to: /tmp/Rtmp73dIua/t3
--- Running overlap_heatmap() ---
Warning: fill_diag must =NULL due to a known bug in the package 'heatmaply'.
Genreating precision-recall matrix.
overlap_heatmap(): Done in 3.5s.
--- Running overlap_heatmap() ---
Genreating precision-recall matrix.
overlap_heatmap(): Done in 0.2s.
--- Running overlap_stat_plot() ---
Preparing reference.
Extracting only the first GRanges object from list.
Done.
--- Running overlap_stat_plot() ---
Preparing reference.
Extracting only the first GRanges object from list.
Done.
--- Running peak_info() ---
Done.
Standardising peak files in 647,114 bins of 5,000 bp.
Merging data into matrix.
Binned matrix size: 647,114 x 3
Matrix sparsity: 0.996
Calculating correlation matrix.
Done computing correlations in 5 seconds.
Saving correlation results ==> /tmp/Rtmp73dIua/file2fcb155339808e.corr.csv.gz
Threshold=0: Filtering peaks
Threshold=0.05: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.1: Filtering peaks
Threshold=0.15: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.2: Filtering peaks
Threshold=0.25: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.3: Filtering peaks
Threshold=0.35: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.4: Filtering peaks
Threshold=0.45: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.5: Filtering peaks
Threshold=0.55: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.6: Filtering peaks
Threshold=0.65: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.7: Filtering peaks
Threshold=0.75: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.8: Filtering peaks
Threshold=0.85: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.9: Filtering peaks
Threshold=0.95: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Reformatting precision-recall data.
Saving precision-recall results ==> /tmp/Rtmp73dIua/file2fcb1572907853precision_recall.csv
Plotting precision-recall curve.
WARNING: 'CnT_missing' missing threshold col, will be excluded from precision-recall calculations.
Standardising peak files in 647,114 bins of 5,000 bp.
Merging data into matrix.
Converting to sparse matrix.
Binned matrix size: 647,114 x 2
Matrix sparsity: 0.9968
WARNING: 'CnT_missing' missing threshold col, will be excluded from precision-recall calculations.
Standardising peak files in 416,959 bins of 5,000 bp.
Merging data into matrix.
Converting to sparse matrix.
Binned matrix size: 416,959 x 2
Matrix sparsity: 0.995
--- Running tss_plot() ---
>> Running bootstrapping for tag matrix...		 2025-09-22 23:43:37 
>> Running bootstrapping for tag matrix...		 2025-09-22 23:43:37 
Done.
--- Running width_boxplot() ---
Done.
[ FAIL 2 | WARN 5 | SKIP 0 | PASS 81 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-EpiCompare.R:16:3'): EpiCompare works ──────────────────────────
Error in `plot_theme(plot)`: The `axis.title.x` theme element must be a <element_text> object.
Backtrace:
     ▆
  1. ├─EpiCompare::EpiCompare(...) at test-EpiCompare.R:16:3
  2. │ └─rmarkdown::render(...)
  3. │   └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  4. │     └─knitr:::process_file(text, output)
  5. │       ├─xfun:::handle_error(...)
  6. │       ├─base::withCallingHandlers(...)
  7. │       └─knitr:::process_group(group)
  8. │         └─knitr:::call_block(x)
  9. │           └─knitr:::block_exec(params)
 10. │             └─knitr:::eng_r(options)
 11. │               ├─knitr:::in_input_dir(...)
 12. │               │ └─knitr:::in_dir(input_dir(), expr)
 13. │               └─knitr (local) evaluate(...)
 14. │                 └─evaluate::evaluate(...)
 15. │                   ├─base::withRestarts(...)
 16. │                   │ └─base (local) withRestartList(expr, restarts)
 17. │                   │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 18. │                   │   │ └─base (local) doWithOneRestart(return(expr), restart)
 19. │                   │   └─base (local) withRestartList(expr, restarts[-nr])
 20. │                   │     └─base (local) withOneRestart(expr, restarts[[1L]])
 21. │                   │       └─base (local) doWithOneRestart(return(expr), restart)
 22. │                   ├─evaluate:::with_handlers(...)
 23. │                   │ ├─base::eval(call)
 24. │                   │ │ └─base::eval(call)
 25. │                   │ └─base::withCallingHandlers(...)
 26. │                   └─watcher$print_value(ev$value, ev$visible, envir)
 27. │                     ├─base::withVisible(handle_value(handler, value, visible, envir))
 28. │                     └─evaluate:::handle_value(handler, value, visible, envir)
 29. │                       └─handler$value(value, visible)
 30. │                         └─knitr (local) fun(x, options = options)
 31. │                           ├─base::withVisible(knit_print(x, ...))
 32. │                           ├─knitr::knit_print(x, ...)
 33. │                           └─knitr:::knit_print.default(x, ...)
 34. │                             └─knitr::normal_print(x)
 35. │                               ├─base::print(x)
 36. │                               └─base::print.default(x)
 37. ├─base (local) `<fn>`(x)
 38. └─patchwork:::print.patchwork(x)
 39.   └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
 40.     └─base::lapply(x$plots, plot_table, guides = guides)
 41.       ├─patchwork (local) FUN(X[[i]], ...)
 42.       └─patchwork:::plot_table.ggplot(X[[i]], ...)
 43.         └─ggplot2::ggplotGrob(x)
 44.           ├─ggplot2::ggplot_gtable(ggplot_build(x))
 45.           │ └─ggplot2:::attach_plot_env(data@plot@plot_env)
 46.           │   └─base::options(ggplot2_plot_env = env)
 47.           ├─ggplot2::ggplot_build(x)
 48.           └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
 49.             └─ggplot2:::plot_theme(plot)
 50.               └─ggplot2:::check_theme(theme)
 51.                 └─base::mapply(...)
 52.                   └─ggplot2 (local) `<fn>`(...)
 53.                     └─cli::cli_abort(...)
 54.                       └─rlang::abort(...)
── Error ('test-plot_precision_recall.R:9:5'): plot_precision_recall works ─────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0 and is now defunct.
i Please use the `rows` argument instead.
Backtrace:
    ▆
 1. └─EpiCompare::plot_precision_recall(...) at test-plot_precision_recall.R:9:5
 2.   └─EpiCompare:::plot_precision_recall_prcurve(...)
 3.     └─ggplot2::facet_grid(facets = facets)
 4.       └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
 5.         └─lifecycle:::deprecate_stop0(msg)
 6.           └─rlang::cnd_signal(...)

[ FAIL 2 | WARN 5 | SKIP 0 | PASS 81 ]
Error: Test failures
Execution halted