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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EpiCompare_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/EpiCompare.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiCompare/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EpiCompare’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 ...Warning: program compiled against libxml 212 using older 211
 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:74-75: 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:82-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:85-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:179: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:181: 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:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:43-44: 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
plot_enrichment            61.411  1.901  66.066
plot_ChIPseeker_annotation 28.545  0.754  29.654
EpiCompare                 14.158  0.740  26.135
rebin_peaks                 9.588  3.033   5.180
plot_precision_recall       9.545  2.014   6.520
predict_precision_recall    8.574  1.793   5.181
plot_corr                   8.778  1.518   8.152
plot_chromHMM               6.349  0.836  46.950
precision_recall            4.275  0.845   5.285
liftover_grlist             4.291  0.592   8.204
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL EpiCompare
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘EpiCompare’ ...
** 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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
output file: EpiCompare.knit.md

/home/biocbuild/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/tmp/RtmpOcE6AE/t1/EpiCompare.html --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/R/R-4.5.0-devel_2024-11-24/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 /home/biocbuild/tmp/RtmpOcE6AE/rmarkdown-str27a7f85d81e47.html --variable code_folding=hide --variable code_menu=1 
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'EpiCompare.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".

Output created: /home/biocbuild/tmp/RtmpOcE6AE/t1/EpiCompare.html
[1] "Done in 2.99 min."
All outputs saved to: /home/biocbuild/tmp/RtmpOcE6AE/t1
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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 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 0.61 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 3 seconds.
Saving correlation results ==> /home/biocbuild/tmp/RtmpOcE6AE/file27a7f85acc804.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 3 seconds.
Saving correlation results ==> /home/biocbuild/tmp/RtmpOcE6AE/file27a7f8478d7e7.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 6 seconds.
Saving correlation results ==> /home/biocbuild/tmp/RtmpOcE6AE/file27a7f840efdb28.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 10 seconds.
Saving correlation results ==> /home/biocbuild/tmp/RtmpOcE6AE/file27a7f85267565e.corr.csv.gz
--- Running fragment_info() ---
Done.
Writing ==> /home/biocbuild/tmp/RtmpOcE6AE/processed_results/encode_H3K27ac.narrowPeaks.bed
Writing ==> /home/biocbuild/tmp/RtmpOcE6AE/processed_results/CnT_H3K27ac.narrowPeaks.bed
Writing ==> /home/biocbuild/tmp/RtmpOcE6AE/processed_results/CnR_H3K27ac.narrowPeaks.bed
Searching for *.narrowPeaks.bed$ files...
3 matching files identified.
Constructing file names.
Importing files.
Reading narrowPeaks
Reading narrowPeaks