##############################################################################
##############################################################################
###
### 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_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/EpiCompare.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiCompare/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EpiCompare’ version ‘1.12.2’
* 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:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_precision_recall.Rd:52-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_precision_recall.Rd:56-58: 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: EpiCompare
> ### Title: Compare epigenomic datasets
> ### Aliases: EpiCompare
> 
> ### ** Examples
> 
> ### Load Data ###
> data("encode_H3K27ac") # example dataset as GRanges object
> data("CnT_H3K27ac") # example dataset as GRanges object
> data("CnR_H3K27ac") # example dataset as GRanges object
> data("CnT_H3K27ac_picard") # example Picard summary output
> data("CnR_H3K27ac_picard") # example Picard summary output
> 
> #### Prepare Input ####
> # create named list of peakfiles
> peakfiles <- list(CnR=CnR_H3K27ac, CnT=CnT_H3K27ac)
> # create named list of picard outputs
> picard_files <- list(CnR=CnR_H3K27ac_picard, CnT=CnT_H3K27ac_picard)
> # reference peak file
> reference <- list("ENCODE" = encode_H3K27ac)
> 
> ### Run EpiCompare ###
> output_html <- EpiCompare(peakfiles = peakfiles,
+            genome_build = list(peakfiles="hg19",
+                                reference="hg19"),
+            picard_files = picard_files,
+            reference = reference,
+            output_filename = "EpiCompare_test",
+            output_dir = tempdir())
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
Error in pm[[2]] : subscript out of bounds
Calls: EpiCompare ... as_interactive -> <Anonymous> -> ggplotly.ggplot -> gg2list

Quitting from EpiCompare.Rmd:278-295 [width_boxplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `pm[[2]]`:
! subscript out of bounds
---
Backtrace:
    ▆
 1. └─EpiCompare::width_boxplot(peaklist = peaklist_tidy, interact = params$interact)
 2.   └─EpiCompare:::as_interactive(boxplot)
 3.     ├─plotly::ggplotly(plt)
 4.     └─plotly:::ggplotly.ggplot(plt)
 5.       └─plotly::gg2list(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
* 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:
    1. ├─EpiCompare::overlap_heatmap(peaklist = peaklist, interact = TRUE) at test-overlap_heatmap.R:8:3
    2. │ └─EpiCompare:::heatmap_heatmaply(X = overlap_matrix)
    3. │   ├─heatmaply::heatmaply(...)
    4. │   └─heatmaply:::heatmaply.default(...)
    5. │     ├─heatmaply::heatmaply(...)
    6. │     └─heatmaply:::heatmaply.heatmapr(...)
    7. │       ├─... %>% layout(showlegend = FALSE)
    8. │       ├─plotly::ggplotly(...)
    9. │       └─plotly:::ggplotly.ggplot(...)
   10. │         └─plotly::gg2list(...)
   11. └─plotly::layout(., showlegend = FALSE)
  
  [ FAIL 5 | WARN 1 | SKIP 0 | PASS 81 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/EpiCompare.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL EpiCompare
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘EpiCompare’ ...
** this is package ‘EpiCompare’ version ‘1.12.2’
** 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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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")
NOTE: The installed version of ComplexUpset package is not yet compatible with ggplot2 >= v4.0.0. Please downgrade to ggplot2 v3 to use this feature. EpiCompare will proceed without generating upset plot. 
 
NOTE: The following EpiCompare features are NOT being used: 
 - upset_plot=
 - add_download_button=
WARNING: precision-recall curves cannot be generated when reference=NULL.


processing file: EpiCompare.Rmd

Quitting from EpiCompare.Rmd:278-295 [width_boxplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `pm[[2]]`:
! subscript out of bounds
---
Backtrace:
     x
  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.   |                 +-base::withVisible(eval(expr, envir))
 27.   |                 \-base::eval(expr, envir)
 28.   |                   \-base::eval(expr, envir)
 29.   \-EpiCompare::width_boxplot(peaklist = peaklist_tidy, interact = params$interact)
 30.     \-EpiCompare:::as_interactive(boxplot)
 31.       +-plotly::ggplotly(plt)
 32.       \-plotly:::ggplotly.ggplot(plt)
 33.         \-plotly::gg2list(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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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 0.78 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/RtmpZgFJRc/filecd98e70ca066b.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 4 seconds.
Saving correlation results ==> /home/biocbuild/tmp/RtmpZgFJRc/filecd98e51f20bd6.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/RtmpZgFJRc/filecd98e43dccc88.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 ==> /home/biocbuild/tmp/RtmpZgFJRc/filecd98ef88708b.corr.csv.gz
--- Running fragment_info() ---
Done.
Writing ==> /home/biocbuild/tmp/RtmpZgFJRc/processed_results/encode_H3K27ac.narrowPeaks.bed
Writing ==> /home/biocbuild/tmp/RtmpZgFJRc/processed_results/CnT_H3K27ac.narrowPeaks.bed
Writing ==> /home/biocbuild/tmp/RtmpZgFJRc/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 ==> /home/biocbuild/tmp/RtmpZgFJRc/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

Quitting from EpiCompare.Rmd:278-295 [width_boxplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `pm[[2]]`:
! subscript out of bounds
---
Backtrace:
     x
  1. \-EpiCompare::EpiCompare(...) at test-output_files.R:10:3
  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.   |                 +-base::withVisible(eval(expr, envir))
 27.   |                 \-base::eval(expr, envir)
 28.   |                   \-base::eval(expr, envir)
 29.   \-EpiCompare::width_boxplot(peaklist = peaklist_tidy, interact = params$interact)
 30.     \-EpiCompare:::as_interactive(boxplot)
 31.       +-plotly::ggplotly(plt)
 32.       \-plotly:::ggplotly.ggplot(plt)
 33.         \-plotly::gg2list(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

Quitting from EpiCompare.Rmd:278-295 [width_boxplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `pm[[2]]`:
! subscript out of bounds
---
Backtrace:
     x
  1. \-EpiCompare::EpiCompare(...) at test-output_files.R:23:3
  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.   |                 +-base::withVisible(eval(expr, envir))
 27.   |                 \-base::eval(expr, envir)
 28.   |                   \-base::eval(expr, envir)
 29.   \-EpiCompare::width_boxplot(peaklist = peaklist_tidy, interact = params$interact)
 30.     \-EpiCompare:::as_interactive(boxplot)
 31.       +-plotly::ggplotly(plt)
 32.       \-plotly:::ggplotly.ggplot(plt)
 33.         \-plotly::gg2list(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

Quitting from EpiCompare.Rmd:278-295 [width_boxplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `pm[[2]]`:
! subscript out of bounds
---
Backtrace:
     x
  1. \-EpiCompare::EpiCompare(...) at test-output_files.R:33:3
  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.   |                 +-base::withVisible(eval(expr, envir))
 27.   |                 \-base::eval(expr, envir)
 28.   |                   \-base::eval(expr, envir)
 29.   \-EpiCompare::width_boxplot(peaklist = peaklist_tidy, interact = params$interact)
 30.     \-EpiCompare:::as_interactive(boxplot)
 31.       +-plotly::ggplotly(plt)
 32.       \-plotly:::ggplotly.ggplot(plt)
 33.         \-plotly::gg2list(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

--- Running overlap_heatmap() ---
Warning: fill_diag must =NULL due to a known bug in the package 'heatmaply'.
Genreating precision-recall matrix.
--- 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 9 seconds.
Saving correlation results ==> /home/biocbuild/tmp/RtmpZgFJRc/filecd98e4848839.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=0.55: 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=0.75: Filtering peaks
Threshold=0.7: 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 ==> /home/biocbuild/tmp/RtmpZgFJRc/filecd98e285bd174precision_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...		 2025-10-14 09:03:40 
>> Running bootstrapping for tag matrix...		 2025-10-14 09:03:41 
Done.
--- Running width_boxplot() ---
Done.
[ FAIL 5 | WARN 1 | SKIP 0 | PASS 81 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-EpiCompare.R:16:3'): EpiCompare works ──────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
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.   │                 ├─base::withVisible(eval(expr, envir))
 27.   │                 └─base::eval(expr, envir)
 28.   │                   └─base::eval(expr, envir)
 29.   └─EpiCompare::width_boxplot(peaklist = peaklist_tidy, interact = params$interact)
 30.     └─EpiCompare:::as_interactive(boxplot)
 31.       ├─plotly::ggplotly(plt)
 32.       └─plotly:::ggplotly.ggplot(plt)
 33.         └─plotly::gg2list(...)
── Error ('test-output_files.R:10:3'): outputs are saved in EpiCompare_file ────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
     ▆
  1. └─EpiCompare::EpiCompare(...) at test-output_files.R:10:3
  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.   │                 ├─base::withVisible(eval(expr, envir))
 27.   │                 └─base::eval(expr, envir)
 28.   │                   └─base::eval(expr, envir)
 29.   └─EpiCompare::width_boxplot(peaklist = peaklist_tidy, interact = params$interact)
 30.     └─EpiCompare:::as_interactive(boxplot)
 31.       ├─plotly::ggplotly(plt)
 32.       └─plotly:::ggplotly.ggplot(plt)
 33.         └─plotly::gg2list(...)
── Error ('test-output_files.R:23:3'): outputs are saved in EpiCompare_file ────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
     ▆
  1. └─EpiCompare::EpiCompare(...) at test-output_files.R:23:3
  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.   │                 ├─base::withVisible(eval(expr, envir))
 27.   │                 └─base::eval(expr, envir)
 28.   │                   └─base::eval(expr, envir)
 29.   └─EpiCompare::width_boxplot(peaklist = peaklist_tidy, interact = params$interact)
 30.     └─EpiCompare:::as_interactive(boxplot)
 31.       ├─plotly::ggplotly(plt)
 32.       └─plotly:::ggplotly.ggplot(plt)
 33.         └─plotly::gg2list(...)
── Error ('test-output_files.R:33:3'): output filename set by users ────────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
     ▆
  1. └─EpiCompare::EpiCompare(...) at test-output_files.R:33:3
  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.   │                 ├─base::withVisible(eval(expr, envir))
 27.   │                 └─base::eval(expr, envir)
 28.   │                   └─base::eval(expr, envir)
 29.   └─EpiCompare::width_boxplot(peaklist = peaklist_tidy, interact = params$interact)
 30.     └─EpiCompare:::as_interactive(boxplot)
 31.       ├─plotly::ggplotly(plt)
 32.       └─plotly:::ggplotly.ggplot(plt)
 33.         └─plotly::gg2list(...)
── Error ('test-overlap_heatmap.R:8:3'): overlap_heatmap works ─────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
     ▆
  1. ├─EpiCompare::overlap_heatmap(peaklist = peaklist, interact = TRUE) at test-overlap_heatmap.R:8:3
  2. │ └─EpiCompare:::heatmap_heatmaply(X = overlap_matrix)
  3. │   ├─heatmaply::heatmaply(...)
  4. │   └─heatmaply:::heatmaply.default(...)
  5. │     ├─heatmaply::heatmaply(...)
  6. │     └─heatmaply:::heatmaply.heatmapr(...)
  7. │       ├─... %>% layout(showlegend = FALSE)
  8. │       ├─plotly::ggplotly(...)
  9. │       └─plotly:::ggplotly.ggplot(...)
 10. │         └─plotly::gg2list(...)
 11. └─plotly::layout(., showlegend = FALSE)

[ FAIL 5 | WARN 1 | SKIP 0 | PASS 81 ]
Error: Test failures
Execution halted