##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiCompare_1.6.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/EpiCompare.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiCompare/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EpiCompare’ version ‘1.6.7’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
plot_enrichment            50.817  3.349  61.543
plot_ChIPseeker_annotation 25.702  0.864  26.631
predict_precision_recall   13.090  3.961   4.587
EpiCompare                 10.218  0.881  11.625
plot_corr                   8.364  1.860   8.546
plot_precision_recall       7.457  2.207   5.517
rebin_peaks                 4.942  1.783   4.901
liftover_grlist             4.485  0.714   7.037
tss_plot                    4.497  0.671   5.182
* 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:
   33.       ├─patchwork (local) FUN(X[[i]], ...)
   34.       └─patchwork:::plot_table.ggplot(X[[i]], ...)
   35.         └─ggplot2::ggplotGrob(x)
   36.           ├─ggplot2::ggplot_gtable(ggplot_build(x))
   37.           └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x))
   38.             └─ggplot2:::plot_theme(plot)
   39.               └─ggplot2:::validate_theme(theme)
   40.                 └─base::mapply(...)
   41.                   └─ggplot2 (local) `<fn>`(...)
   42.                     └─cli::cli_abort(...)
   43.                       └─rlang::abort(...)
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 78 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/EpiCompare.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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

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

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

> 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 lines 345-359 [overlap_upset_plot] (EpiCompare.Rmd)
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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/RtmpY2eG86/file5a80237a7c36.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 ==> /tmp/RtmpY2eG86/file5a803e70cf6c.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 5 seconds.
Saving correlation results ==> /tmp/RtmpY2eG86/file5a806041db7a.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 11 seconds.
Saving correlation results ==> /tmp/RtmpY2eG86/file5a803b057f5.corr.csv.gz
--- Running fragment_info() ---
Done.
Writing ==> /tmp/RtmpY2eG86/processed_results/encode_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/RtmpY2eG86/processed_results/CnT_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/RtmpY2eG86/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/RtmpY2eG86/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

/opt/homebrew/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/tmp/RtmpY2eG86/t1/EpiCompare.html --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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/RtmpY2eG86/rmarkdown-str5a803e07af15.html --variable code_folding=hide --variable code_menu=1 

Output created: /private/tmp/RtmpY2eG86/t1/EpiCompare.html
[1] "Done in 0.12 min."
All outputs saved to: /tmp/RtmpY2eG86/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

/opt/homebrew/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/tmp/RtmpY2eG86/t2/EpiCompare.html --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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/RtmpY2eG86/rmarkdown-str5a8057bf0352.html --variable code_folding=hide --variable code_menu=1 

Output created: /private/tmp/RtmpY2eG86/t2/EpiCompare.html
[1] "Done in 0.13 min."
All outputs saved to: /tmp/RtmpY2eG86/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

/opt/homebrew/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/tmp/RtmpY2eG86/t3/testthat_example_Apr_17_2024.html --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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/RtmpY2eG86/rmarkdown-str5a801a447955.html --variable code_folding=hide --variable code_menu=1 

Output created: /private/tmp/RtmpY2eG86/t3/testthat_example_Apr_17_2024.html
[1] "Done in 0.13 min."
All outputs saved to: /tmp/RtmpY2eG86/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 3.4s.
--- Running overlap_heatmap() ---
Genreating precision-recall matrix.
overlap_heatmap(): Done in 0.1s.
--- 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 6 seconds.
Saving correlation results ==> /tmp/RtmpY2eG86/file5a802ce918b0.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=0.35: Filtering peaks
Threshold=0.3: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.45: Filtering peaks
Threshold=0.4: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.55: Filtering peaks
Threshold=0.5: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.65: Filtering peaks
Threshold=0.6: 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=0.85: Filtering peaks
Threshold=0.8: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.95: Filtering peaks
Threshold=0.9: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Reformatting precision-recall data.
Saving precision-recall results ==> /tmp/RtmpY2eG86/file5a8075adac72precision_recall.csv
Plotting precision-recall curve.
Plotting F1.
Making predictions for peaklist1: CnR_H3K27ac
Making predictions for peaklist2: encode_H3K27ac
+ Predicting recall from 10 precision values.
+ Predicting precision from 10 recall values.
Making predictions for peaklist1: CnT_H3K27ac
Making predictions for peaklist2: encode_H3K27ac
+ Predicting recall from 10 precision values.
+ Predicting precision from 10 recall values.
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...		 2024-04-17 13:10:24 
>> Running bootstrapping for tag matrix...		 2024-04-17 13:10:25 
Done.
--- Running width_boxplot() ---
Done.
[ FAIL 1 | WARN 7 | SKIP 0 | PASS 78 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-EpiCompare.R:16:3'): EpiCompare works ──────────────────────────
Error in `plot_theme(plot)`: The `legend.text.align` theme element is not defined in the element hierarchy.
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. │       ├─knitr:::handle_error(...)
  6. │       │ └─base::withCallingHandlers(...)
  7. │       ├─base::withCallingHandlers(...)
  8. │       ├─knitr:::process_group(group)
  9. │       └─knitr:::process_group.block(group)
 10. │         └─knitr:::call_block(x)
 11. │           └─knitr:::block_exec(params)
 12. │             └─knitr:::eng_r(options)
 13. │               ├─knitr:::in_input_dir(...)
 14. │               │ └─knitr:::in_dir(input_dir(), expr)
 15. │               └─knitr (local) evaluate(...)
 16. │                 └─evaluate::evaluate(...)
 17. │                   └─evaluate:::evaluate_call(...)
 18. │                     ├─base (local) handle(...)
 19. │                     ├─base::withCallingHandlers(...)
 20. │                     ├─base::withVisible(value_fun(ev$value, ev$visible))
 21. │                     └─knitr (local) value_fun(ev$value, ev$visible)
 22. │                       └─knitr (local) fun(x, options = options)
 23. │                         ├─base::withVisible(knit_print(x, ...))
 24. │                         ├─knitr::knit_print(x, ...)
 25. │                         └─knitr:::knit_print.default(x, ...)
 26. │                           └─evaluate (local) normal_print(x)
 27. │                             ├─base::print(x)
 28. │                             └─base::print.default(x)
 29. ├─base (local) `<fn>`(x)
 30. └─patchwork:::print.patchwork(x)
 31.   └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
 32.     └─base::lapply(x$plots, plot_table, guides = guides)
 33.       ├─patchwork (local) FUN(X[[i]], ...)
 34.       └─patchwork:::plot_table.ggplot(X[[i]], ...)
 35.         └─ggplot2::ggplotGrob(x)
 36.           ├─ggplot2::ggplot_gtable(ggplot_build(x))
 37.           └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x))
 38.             └─ggplot2:::plot_theme(plot)
 39.               └─ggplot2:::validate_theme(theme)
 40.                 └─base::mapply(...)
 41.                   └─ggplot2 (local) `<fn>`(...)
 42.                     └─cli::cli_abort(...)
 43.                       └─rlang::abort(...)

[ FAIL 1 | WARN 7 | SKIP 0 | PASS 78 ]
Error: Test failures
Execution halted