##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings EpiCompare_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/EpiCompare.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* 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 ... 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 ... ERROR
Running examples in ‘EpiCompare-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute_corr
> ### Title: Compute correlation matrix
> ### Aliases: compute_corr
> 
> ### ** 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)
> 
> #increasing bin_size for speed but lower values will give more granular corr
> corr_mat <- compute_corr(peakfiles = peakfiles,
+                          reference = reference,
+                          genome_build = "hg19",
+                          bin_size = 200000, 
+                          workers = 1)
Standardising peak files in 16,318 bins of 2e+05 bp.

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(v, na.rm = na.rm)
 3: viewMeans(v, na.rm = na.rm)
 4: viewMeans2(v, na.rm = na.rm)
 5: FUN(X[[i]], ...)
 6: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 7: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,     varname = "score", na.rm = FALSE)
 9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: apply_fun(FUN = FUN, X, ...)
20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) {    gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols,         initial_threshold = 0)    gr_names <- names(GenomicRanges::mcols(gr))    intens_col <- gr_names[gr_names %in% paste(intensity_cols,         "percentile", sep = "_")][1]    data_cov <- GenomicRanges::coverage(gr, weight = intens_col)    rm(gr)    gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,         varname = "score", na.rm = FALSE)    return(gr$score)}, ...)
21: rebin_peaks(peakfiles = all_peaks, genome_build = genome_build,     keep_chr = keep_chr, drop_empty_chr = drop_empty_chr, intensity_cols = intensity_cols,     bin_size = bin_size, as_sparse = FALSE, workers = workers)
22: compute_corr(peakfiles = peakfiles, reference = reference, genome_build = "hg19",     bin_size = 2e+05, workers = 1)
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(v, na.rm = na.rm)
 3: viewMeans(v, na.rm = na.rm)
 4: viewMeans2(v, na.rm = na.rm)
 5: FUN(X[[i]], ...)
 6: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 7: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,     varname = "score", na.rm = FALSE)
 9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: apply_fun(FUN = FUN, X, ...)
20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) {    gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols,         initial_threshold = 0)    gr_names <- names(GenomicRanges::mcols(gr))    intens_col <- gr_names[gr_names %in% paste(intensity_cols,         "percentile", sep = "_")][1]    data_cov <- GenomicRanges::coverage(gr, weight = intens_col)    rm(gr)    gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,         varname = "score", na.rm = FALSE)    return(gr$score)}, ...)
21: rebin_peaks(peakfiles = all_peaks, genome_build = genome_build,     keep_chr = keep_chr, drop_empty_chr = drop_empty_chr, intensity_cols = intensity_cols,     bin_size = bin_size, as_sparse = FALSE, workers = workers)
22: compute_corr(peakfiles = peakfiles, reference = reference, genome_build = "hg19",     bin_size = 2e+05, workers = 1)
An irrecoverable exception occurred. R is aborting now ...
Warning in apply_fun(FUN = FUN, X, ...) :
  scheduled cores 1, 2 did not deliver results, all values of the jobs will be affected
Merging data into matrix.
Error in `rownames<-`(`*tmp*`, value = paste0(GenomicRanges::seqnames(gr_windows),  : 
  attempt to set 'rownames' on an object with no dimensions
Calls: compute_corr -> rebin_peaks -> rownames<-
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
EpiCompare 18.315  2.556  23.186
* 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::plot_corr(...) at test-plot_corr.R:9:5
   2.   └─EpiCompare::compute_corr(...)
   3.     └─EpiCompare::rebin_peaks(...)
   4.       └─base::`rownames<-`(...)
  ── Error ('test-rebin_peaks.R:13:5'): rebin_peaks works ────────────────────────
  Error in ``rownames<-`(`*tmp*`, value = paste0(GenomicRanges::seqnames(gr_windows), 
      sep[1], GenomicRanges::start(gr_windows), sep[2], GenomicRanges::end(gr_windows)))`: attempt to set 'rownames' on an object with no dimensions
  Backtrace:
      ▆
   1. └─EpiCompare::rebin_peaks(...) at test-rebin_peaks.R:13:5
   2.   └─base::`rownames<-`(...)
  
  [ FAIL 4 | WARN 10 | SKIP 0 | PASS 77 ]
  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-3.21-bioc/meat/EpiCompare.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL EpiCompare
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘EpiCompare’ ...
** this is package ‘EpiCompare’ version ‘1.11.0’
** 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) (2025-01-20 r87609) -- "Unsuffered Consequences"
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

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(v, na.rm = na.rm)
 3: viewMeans(v, na.rm = na.rm)
 4: viewMeans2(v, na.rm = na.rm)
 5: FUN(X[[i]], ...)
 6: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 7: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,     varname = "score", na.rm = FALSE)
 9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: apply_fun(FUN = FUN, X, ...)
20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) {    gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols,         initial_threshold = 0)    gr_names <- names(GenomicRanges::mcols(gr))    intens_col <- gr_names[gr_names %in% paste(intensity_cols,         "percentile", sep = "_")][1]    data_cov <- GenomicRanges::coverage(gr, weight = intens_col)    rm(gr)    gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,         varname = "score", na.rm = FALSE)    return(gr$score)}, ...)
21: rebin_peaks(peakfiles = all_peaks, genome_build = genome_build,     keep_chr = keep_chr, drop_empty_chr = drop_empty_chr, intensity_cols = intensity_cols,     bin_size = bin_size, as_sparse = FALSE, workers = workers)
22: compute_corr(peakfiles = peakfiles, reference = reference, genome_build = genome_build,     bin_size = bin_size, keep_chr = keep_chr, drop_empty_chr = drop_empty_chr,     method = method, intensity_cols = intensity_cols, fill_diag = fill_diag,     workers = workers, save_path = save_path)
23: plot_corr(peakfiles = peaklist_tidy, reference = reference_tidy,     genome_build = output_build, bin_size = params$bin_size,     workers = params$workers, show_plot = FALSE, save_path = save_path,     interact = params$interact)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
47: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
48: process_file(text, output)
49: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
50: rmarkdown::render(input = markdown_path, output_dir = output_dir,     output_file = output_filename, quiet = quiet, params = list(peakfiles = peakfiles,         genome_build = genome_build, genome_build_output = genome_build_output,         blacklist = blacklist, picard_files = picard_files, reference = reference,         upset_plot = upset_plot, stat_plot = stat_plot, chromHMM_plot = chromHMM_plot,         chromHMM_annotation = chromHMM_annotation, chipseeker_plot = chipseeker_plot,         enrichment_plot = enrichment_plot, tss_plot = tss_plot,         tss_distance = tss_distance, precision_recall_plot = precision_recall_plot,         n_threshold = n_threshold, corr_plot = corr_plot, bin_size = bin_size,         interact = interact, add_download_button = add_download_button,         save_output = save_output, output_dir = output_dir, workers = workers,         error = error, debug = debug))
51: EpiCompare::EpiCompare(peakfiles = peaklist, genome_build = "hg19",     picard_files = picard_list, reference = NULL, interact = TRUE,     tss_distance = c(-50, 50), run_all = TRUE, output_dir = outpath)
52: eval(code, test_env)
53: eval(code, test_env)
54: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
55: doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchOne(expr, names, parentenv, handlers[[1L]])
57: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
58: doTryCatch(return(expr), name, parentenv, handler)
59: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
60: tryCatchList(expr, classes, parentenv, handlers)
61: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
62: test_code(desc, code, env = parent.frame(), reporter = reporter)
63: testthat::test_that("EpiCompare works", {    {        data("encode_H3K27ac")        data("CnT_H3K27ac")        data("CnR_H3K27ac")        data("CnT_H3K27ac_picard")        data("CnR_H3K27ac_picard")        peaklist <- list(CnT = CnT_H3K27ac, CnR = CnR_H3K27ac)        reference <- list(ENCODE = encode_H3K27ac)        picard_list <- list(CnT = CnT_H3K27ac_picard, CnR = CnR_H3K27ac_picard)    }    outpath <- file.path(tempdir(), "t1")    html_file <- EpiCompare::EpiCompare(peakfiles = peaklist,         genome_build = "hg19", picard_files = picard_list, reference = NULL,         interact = TRUE, tss_distance = c(-50, 50), run_all = TRUE,         output_dir = outpath)    files <- list.files(file.path(outpath, "EpiCompare_file"))    testthat::expect_gte(length(files), 10)    testthat::expect_true(is.element("peak_info.csv", files))    testthat::expect_true(is.element("fragment_info.csv", files))    testthat::expect_true(is.element("width_plot.html", files))    testthat::expect_true(is.element("samples_percent_overlap.html",         files))    testthat::expect_false(is.element("stat_plot.png", files))    testthat::expect_true(is.element("samples_ChromHMM.html",         files))    testthat::expect_false(is.element("sample_in_ref_ChromHMM.html",         files))    testthat::expect_false(is.element("ref_in_sample_ChromHMM.html",         files))    testthat::expect_false(is.element("ref_not_in_sample_ChromHMM.html",         files))    testthat::expect_false(is.element("sample_not_in_ref_ChromHMM.html",         files))    testthat::expect_true(is.element("chipseeker_annotation.html",         files))    testthat::expect_true(is.element("KEGG_analysis.html", files))    testthat::expect_true(is.element("GO_analysis.html", files))})
64: eval(code, test_env)
65: eval(code, test_env)
66: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
67: doTryCatch(return(expr), name, parentenv, handler)
68: tryCatchOne(expr, names, parentenv, handlers[[1L]])
69: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
70: doTryCatch(return(expr), name, parentenv, handler)
71: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
72: tryCatchList(expr, classes, parentenv, handlers)
73: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
74: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
75: source_file(path, env = env(env), desc = desc, error_call = error_call)
76: FUN(X[[i]], ...)
77: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
78: doTryCatch(return(expr), name, parentenv, handler)
79: tryCatchOne(expr, names, parentenv, handlers[[1L]])
80: tryCatchList(expr, classes, parentenv, handlers)
81: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
82: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
83: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
84: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
85: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
86: test_check("EpiCompare")
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(v, na.rm = na.rm)
 3: viewMeans(v, na.rm = na.rm)
 4: viewMeans2(v, na.rm = na.rm)
 5: FUN(X[[i]], ...)
 6: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 7: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,     varname = "score", na.rm = FALSE)
 9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: apply_fun(FUN = FUN, X, ...)
20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) {    gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols,         initial_threshold = 0)    gr_names <- names(GenomicRanges::mcols(gr))    intens_col <- gr_names[gr_names %in% paste(intensity_cols,         "percentile", sep = "_")][1]    data_cov <- GenomicRanges::coverage(gr, weight = intens_col)    rm(gr)    gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,         varname = "score", na.rm = FALSE)    return(gr$score)}, ...)
21: rebin_peaks(peakfiles = all_peaks, genome_build = genome_build,     keep_chr = keep_chr, drop_empty_chr = drop_empty_chr, intensity_cols = intensity_cols,     bin_size = bin_size, as_sparse = FALSE, workers = workers)
22: compute_corr(peakfiles = peakfiles, reference = reference, genome_build = genome_build,     bin_size = bin_size, keep_chr = keep_chr, drop_empty_chr = drop_empty_chr,     method = method, intensity_cols = intensity_cols, fill_diag = fill_diag,     workers = workers, save_path = save_path)
23: plot_corr(peakfiles = peaklist_tidy, reference = reference_tidy,     genome_build = output_build, bin_size = params$bin_size,     workers = params$workers, show_plot = FALSE, save_path = save_path,     interact = params$interact)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
47: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
48: process_file(text, output)
49: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
50: rmarkdown::render(input = markdown_path, output_dir = output_dir,     output_file = output_filename, quiet = quiet, params = list(peakfiles = peakfiles,         genome_build = genome_build, genome_build_output = genome_build_output,         blacklist = blacklist, picard_files = picard_files, reference = reference,         upset_plot = upset_plot, stat_plot = stat_plot, chromHMM_plot = chromHMM_plot,         chromHMM_annotation = chromHMM_annotation, chipseeker_plot = chipseeker_plot,         enrichment_plot = enrichment_plot, tss_plot = tss_plot,         tss_distance = tss_distance, precision_recall_plot = precision_recall_plot,         n_threshold = n_threshold, corr_plot = corr_plot, bin_size = bin_size,         interact = interact, add_download_button = add_download_button,         save_output = save_output, output_dir = output_dir, workers = workers,         error = error, debug = debug))
51: EpiCompare::EpiCompare(peakfiles = peaklist, genome_build = "hg19",     picard_files = picard_list, reference = NULL, interact = TRUE,     tss_distance = c(-50, 50), run_all = TRUE, output_dir = outpath)
52: eval(code, test_env)
53: eval(code, test_env)
54: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
55: doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchOne(expr, names, parentenv, handlers[[1L]])
57: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
58: doTryCatch(return(expr), name, parentenv, handler)
59: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
60: tryCatchList(expr, classes, parentenv, handlers)
61: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
62: test_code(desc, code, env = parent.frame(), reporter = reporter)
63: testthat::test_that("EpiCompare works", {    {        data("encode_H3K27ac")        data("CnT_H3K27ac")        data("CnR_H3K27ac")        data("CnT_H3K27ac_picard")        data("CnR_H3K27ac_picard")        peaklist <- list(CnT = CnT_H3K27ac, CnR = CnR_H3K27ac)        reference <- list(ENCODE = encode_H3K27ac)        picard_list <- list(CnT = CnT_H3K27ac_picard, CnR = CnR_H3K27ac_picard)    }    outpath <- file.path(tempdir(), "t1")    html_file <- EpiCompare::EpiCompare(peakfiles = peaklist,         genome_build = "hg19", picard_files = picard_list, reference = NULL,         interact = TRUE, tss_distance = c(-50, 50), run_all = TRUE,         output_dir = outpath)    files <- list.files(file.path(outpath, "EpiCompare_file"))    testthat::expect_gte(length(files), 10)    testthat::expect_true(is.element("peak_info.csv", files))    testthat::expect_true(is.element("fragment_info.csv", files))    testthat::expect_true(is.element("width_plot.html", files))    testthat::expect_true(is.element("samples_percent_overlap.html",         files))    testthat::expect_false(is.element("stat_plot.png", files))    testthat::expect_true(is.element("samples_ChromHMM.html",         files))    testthat::expect_false(is.element("sample_in_ref_ChromHMM.html",         files))    testthat::expect_false(is.element("ref_in_sample_ChromHMM.html",         files))    testthat::expect_false(is.element("ref_not_in_sample_ChromHMM.html",         files))    testthat::expect_false(is.element("sample_not_in_ref_ChromHMM.html",         files))    testthat::expect_true(is.element("chipseeker_annotation.html",         files))    testthat::expect_true(is.element("KEGG_analysis.html", files))    testthat::expect_true(is.element("GO_analysis.html", files))})
64: eval(code, test_env)
65: eval(code, test_env)
66: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
67: doTryCatch(return(expr), name, parentenv, handler)
68: tryCatchOne(expr, names, parentenv, handlers[[1L]])
69: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
70: doTryCatch(return(expr), name, parentenv, handler)
71: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
72: tryCatchList(expr, classes, parentenv, handlers)
73: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
74: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
75: source_file(path, env = env(env), desc = desc, error_call = error_call)
76: FUN(X[[i]], ...)
77: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
78: doTryCatch(return(expr), name, parentenv, handler)
79: tryCatchOne(expr, names, parentenv, handlers[[1L]])
80: tryCatchList(expr, classes, parentenv, handlers)
81: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
82: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
83: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
84: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
85: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
86: test_check("EpiCompare")
An irrecoverable exception occurred. R is aborting now ...

Quitting from lines 459-481 [Correlation 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 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 0.43 min.
Standardising peak files in 6,659 bins of 5e+05 bp.

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(v, na.rm = na.rm)
 3: viewMeans(v, na.rm = na.rm)
 4: viewMeans2(v, na.rm = na.rm)
 5: FUN(X[[i]], ...)
 6: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 7: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,     varname = "score", na.rm = FALSE)
 9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: apply_fun(FUN = FUN, X, ...)
20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) {    gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols,         initial_threshold = 0)    gr_names <- names(GenomicRanges::mcols(gr))    intens_col <- gr_names[gr_names %in% paste(intensity_cols,         "percentile", sep = "_")][1]    data_cov <- GenomicRanges::coverage(gr, weight = intens_col)    rm(gr)    gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,         varname = "score", na.rm = FALSE)    return(gr$score)}, ...)
21: rebin_peaks(peakfiles = all_peaks, genome_build = genome_build,     keep_chr = keep_chr, drop_empty_chr = drop_empty_chr, intensity_cols = intensity_cols,     bin_size = bin_size, as_sparse = FALSE, workers = workers)
22: compute_corr(peakfiles = peakfiles, reference = reference, genome_build = "hg19",     workers = 1, bin_size = bin_size)
23: (function (bin_size) {    compute_corr(peakfiles = peakfiles, reference = reference,         genome_build = "hg19", workers = 1, bin_size = bin_size)})(dots[[1L]][[1L]])
24: mapply(stats::setNames(bins, bins), SIMPLIFY = FALSE, FUN = function(bin_size) {    compute_corr(peakfiles = peakfiles, reference = reference,         genome_build = "hg19", workers = 1, bin_size = bin_size)})
25: eval(code, test_env)
26: eval(code, test_env)
27: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
35: test_code(desc, code, env = parent.frame(), reporter = reporter)
36: test_that("compute_corr works", {    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)    bins <- c(5e+05, 1e+05, 10000, 5000)    cor_mats <- mapply(stats::setNames(bins, bins), SIMPLIFY = FALSE,         FUN = function(bin_size) {            compute_corr(peakfiles = peakfiles, reference = reference,                 genome_build = "hg19", workers = 1, bin_size = bin_size)        })    cor_mats2 <- mapply(cor_mats, SIMPLIFY = FALSE, FUN = function(x) {        diag(x) <- NA        x    })    cor_mean <- mapply(cor_mats2, FUN = mean, na.rm = TRUE)    testthat::expect_equal(round(mean(cor_mean), 2), 0.75)    testthat::expect_gte(cor(as.numeric(names(cor_mean)), cor_mean),         0.85)})
37: eval(code, test_env)
38: eval(code, test_env)
39: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
43: doTryCatch(return(expr), name, parentenv, handler)
44: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
45: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
47: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
48: source_file(path, env = env(env), desc = desc, error_call = error_call)
49: FUN(X[[i]], ...)
50: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
51: doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: tryCatchList(expr, classes, parentenv, handlers)
54: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
55: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
56: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
57: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
58: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
59: test_check("EpiCompare")
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(v, na.rm = na.rm)
 3: viewMeans(v, na.rm = na.rm)
 4: viewMeans2(v, na.rm = na.rm)
 5: FUN(X[[i]], ...)
 6: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 7: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,     varname = "score", na.rm = FALSE)
 9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: apply_fun(FUN = FUN, X, ...)
20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) {    gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols,         initial_threshold = 0)    gr_names <- names(GenomicRanges::mcols(gr))    intens_col <- gr_names[gr_names %in% paste(intensity_cols,         "percentile", sep = "_")][1]    data_cov <- GenomicRanges::coverage(gr, weight = intens_col)    rm(gr)    gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,         varname = "score", na.rm = FALSE)    return(gr$score)}, ...)
21: rebin_peaks(peakfiles = all_peaks, genome_build = genome_build,     keep_chr = keep_chr, drop_empty_chr = drop_empty_chr, intensity_cols = intensity_cols,     bin_size = bin_size, as_sparse = FALSE, workers = workers)
22: compute_corr(peakfiles = peakfiles, reference = reference, genome_build = "hg19",     workers = 1, bin_size = bin_size)
23: (function (bin_size) {    compute_corr(peakfiles = peakfiles, reference = reference,         genome_build = "hg19", workers = 1, bin_size = bin_size)})(dots[[1L]][[1L]])
24: mapply(stats::setNames(bins, bins), SIMPLIFY = FALSE, FUN = function(bin_size) {    compute_corr(peakfiles = peakfiles, reference = reference,         genome_build = "hg19", workers = 1, bin_size = bin_size)})
25: eval(code, test_env)
26: eval(code, test_env)
27: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
35: test_code(desc, code, env = parent.frame(), reporter = reporter)
36: test_that("compute_corr works", {    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)    bins <- c(5e+05, 1e+05, 10000, 5000)    cor_mats <- mapply(stats::setNames(bins, bins), SIMPLIFY = FALSE,         FUN = function(bin_size) {            compute_corr(peakfiles = peakfiles, reference = reference,                 genome_build = "hg19", workers = 1, bin_size = bin_size)        })    cor_mats2 <- mapply(cor_mats, SIMPLIFY = FALSE, FUN = function(x) {        diag(x) <- NA        x    })    cor_mean <- mapply(cor_mats2, FUN = mean, na.rm = TRUE)    testthat::expect_equal(round(mean(cor_mean), 2), 0.75)    testthat::expect_gte(cor(as.numeric(names(cor_mean)), cor_mean),         0.85)})
37: eval(code, test_env)
38: eval(code, test_env)
39: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
43: doTryCatch(return(expr), name, parentenv, handler)
44: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
45: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
47: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
48: source_file(path, env = env(env), desc = desc, error_call = error_call)
49: FUN(X[[i]], ...)
50: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
51: doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: tryCatchList(expr, classes, parentenv, handlers)
54: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
55: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
56: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
57: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
58: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
59: test_check("EpiCompare")
An irrecoverable exception occurred. R is aborting now ...
Merging data into matrix.
--- Running fragment_info() ---
Done.
Writing ==> /tmp/RtmpXvm30N/processed_results/encode_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/RtmpXvm30N/processed_results/CnT_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/RtmpXvm30N/processed_results/CnR_H3K27ac.narrowPeaks.bed
Searching for *.narrowPeaks.bed$ 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/RtmpXvm30N/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/RtmpXvm30N/t1/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-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-3.21-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/RtmpXvm30N/rmarkdown-str2ae45b3b638573.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/RtmpXvm30N/t1/EpiCompare.html
[1] "Done in 0.11 min."
All outputs saved to: /tmp/RtmpXvm30N/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/RtmpXvm30N/t2/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-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-3.21-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/RtmpXvm30N/rmarkdown-str2ae45bdbc8eb6.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/RtmpXvm30N/t2/EpiCompare.html
[1] "Done in 0.12 min."
All outputs saved to: /tmp/RtmpXvm30N/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/RtmpXvm30N/t3/testthat_example_Jan_24_2025.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-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-3.21-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/RtmpXvm30N/rmarkdown-str2ae45b842ab31.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/RtmpXvm30N/t3/testthat_example_Jan_24_2025.html
[1] "Done in 0.11 min."
All outputs saved to: /tmp/RtmpXvm30N/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 3.2s.
--- 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.

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(v, na.rm = na.rm)
 3: viewMeans(v, na.rm = na.rm)
 4: viewMeans2(v, na.rm = na.rm)
 5: FUN(X[[i]], ...)
 6: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 7: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,     varname = "score", na.rm = FALSE)
 9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: apply_fun(FUN = FUN, X, ...)
20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) {    gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols,         initial_threshold = 0)    gr_names <- names(GenomicRanges::mcols(gr))    intens_col <- gr_names[gr_names %in% paste(intensity_cols,         "percentile", sep = "_")][1]    data_cov <- GenomicRanges::coverage(gr, weight = intens_col)    rm(gr)    gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,         varname = "score", na.rm = FALSE)    return(gr$score)}, ...)
21: rebin_peaks(peakfiles = all_peaks, genome_build = genome_build,     keep_chr = keep_chr, drop_empty_chr = drop_empty_chr, intensity_cols = intensity_cols,     bin_size = bin_size, as_sparse = FALSE, workers = workers)
22: compute_corr(peakfiles = peakfiles, reference = reference, genome_build = genome_build,     bin_size = bin_size, keep_chr = keep_chr, drop_empty_chr = drop_empty_chr,     method = method, intensity_cols = intensity_cols, fill_diag = fill_diag,     workers = workers, save_path = save_path)
23: plot_corr(peakfiles = peakfiles, reference = reference, genome_build = "hg19",     workers = 1, bin_size = 5000)
24: eval(code, test_env)
25: eval(code, test_env)
26: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
34: test_code(desc, code, env = parent.frame(), reporter = reporter)
35: test_that("plot_corr works", {    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)    cp_out <- plot_corr(peakfiles = peakfiles, reference = reference,         genome_build = "hg19", workers = 1, bin_size = 5000)    testthat::expect_equal(nrow(cp_out$data), 3)    testthat::expect_equal(round(mean(cp_out$data, na.rm = TRUE),         2), 0.63)    testthat::expect_true(all(c("data", "corr_plot") %in% names(cp_out)))    testthat::expect_true(all(c("CnR_H3K27ac", "CnT_H3K27ac",         "encode_H3K27ac") %in% colnames(cp_out$data)))    testthat::expect_true(methods::is(cp_out$corr_plot, "gg"))})
36: eval(code, test_env)
37: eval(code, test_env)
38: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
41: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
42: doTryCatch(return(expr), name, parentenv, handler)
43: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
44: tryCatchList(expr, classes, parentenv, handlers)
45: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
46: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
47: source_file(path, env = env(env), desc = desc, error_call = error_call)
48: FUN(X[[i]], ...)
49: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
50: doTryCatch(return(expr), name, parentenv, handler)
51: tryCatchOne(expr, names, parentenv, handlers[[1L]])
52: tryCatchList(expr, classes, parentenv, handlers)
53: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
54: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
55: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
56: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
57: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
58: test_check("EpiCompare")
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(v, na.rm = na.rm)
 3: viewMeans(v, na.rm = na.rm)
 4: viewMeans2(v, na.rm = na.rm)
 5: FUN(X[[i]], ...)
 6: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 7: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,     varname = "score", na.rm = FALSE)
 9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: apply_fun(FUN = FUN, X, ...)
20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) {    gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols,         initial_threshold = 0)    gr_names <- names(GenomicRanges::mcols(gr))    intens_col <- gr_names[gr_names %in% paste(intensity_cols,         "percentile", sep = "_")][1]    data_cov <- GenomicRanges::coverage(gr, weight = intens_col)    rm(gr)    gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,         varname = "score", na.rm = FALSE)    return(gr$score)}, ...)
21: rebin_peaks(peakfiles = all_peaks, genome_build = genome_build,     keep_chr = keep_chr, drop_empty_chr = drop_empty_chr, intensity_cols = intensity_cols,     bin_size = bin_size, as_sparse = FALSE, workers = workers)
22: compute_corr(peakfiles = peakfiles, reference = reference, genome_build = genome_build,     bin_size = bin_size, keep_chr = keep_chr, drop_empty_chr = drop_empty_chr,     method = method, intensity_cols = intensity_cols, fill_diag = fill_diag,     workers = workers, save_path = save_path)
23: plot_corr(peakfiles = peakfiles, reference = reference, genome_build = "hg19",     workers = 1, bin_size = 5000)
24: eval(code, test_env)
25: eval(code, test_env)
26: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
34: test_code(desc, code, env = parent.frame(), reporter = reporter)
35: test_that("plot_corr works", {    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)    cp_out <- plot_corr(peakfiles = peakfiles, reference = reference,         genome_build = "hg19", workers = 1, bin_size = 5000)    testthat::expect_equal(nrow(cp_out$data), 3)    testthat::expect_equal(round(mean(cp_out$data, na.rm = TRUE),         2), 0.63)    testthat::expect_true(all(c("data", "corr_plot") %in% names(cp_out)))    testthat::expect_true(all(c("CnR_H3K27ac", "CnT_H3K27ac",         "encode_H3K27ac") %in% colnames(cp_out$data)))    testthat::expect_true(methods::is(cp_out$corr_plot, "gg"))})
36: eval(code, test_env)
37: eval(code, test_env)
38: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
41: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
42: doTryCatch(return(expr), name, parentenv, handler)
43: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
44: tryCatchList(expr, classes, parentenv, handlers)
45: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
46: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
47: source_file(path, env = env(env), desc = desc, error_call = error_call)
48: FUN(X[[i]], ...)
49: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
50: doTryCatch(return(expr), name, parentenv, handler)
51: tryCatchOne(expr, names, parentenv, handlers[[1L]])
52: tryCatchList(expr, classes, parentenv, handlers)
53: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
54: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
55: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
56: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
57: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
58: test_check("EpiCompare")
An irrecoverable exception occurred. R is aborting now ...
Merging data into matrix.
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=0.75: Filtering peaks
Threshold=0.7: 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/RtmpXvm30N/file2ae45b44611d61precision_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.

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(v, na.rm = na.rm)
 3: viewMeans(v, na.rm = na.rm)
 4: viewMeans2(v, na.rm = na.rm)
 5: FUN(X[[i]], ...)
 6: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 7: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,     varname = "score", na.rm = FALSE)
 9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: apply_fun(FUN = FUN, X, ...)
20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) {    gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols,         initial_threshold = 0)    gr_names <- names(GenomicRanges::mcols(gr))    intens_col <- gr_names[gr_names %in% paste(intensity_cols,         "percentile", sep = "_")][1]    data_cov <- GenomicRanges::coverage(gr, weight = intens_col)    rm(gr)    gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,         varname = "score", na.rm = FALSE)    return(gr$score)}, ...)
21: EpiCompare::rebin_peaks(peakfiles = peakfiles, genome_build = "hg19",     bin_size = 5000, workers = 1)
22: eval(code, test_env)
23: eval(code, test_env)
24: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
32: test_code(desc, code, env = parent.frame(), reporter = reporter)
33: test_that("rebin_peaks works", {    data("CnR_H3K27ac")    data("CnT_H3K27ac")    peakfiles <- list(CnR_H3K27ac = CnR_H3K27ac, CnT_H3K27ac = CnT_H3K27ac,         CnT_missing = CnT_H3K27ac)    GenomicRanges::mcols(peakfiles$CnT_missing)$qValue <- NULL    GenomicRanges::mcols(peakfiles$CnT_missing)$score <- NULL    peakfiles_rebinned <- EpiCompare::rebin_peaks(peakfiles = peakfiles,         genome_build = "hg19", bin_size = 5000, workers = 1)    testthat::expect_true(methods::is(peakfiles_rebinned, "Matrix"))    testthat::expect_equal(dim(peakfiles_rebinned), c(647114,         2))    keep_chr <- paste0("chr", seq_len(12))    peakfiles_rebinned2 <- EpiCompare::rebin_peaks(peakfiles = peakfiles,         keep_chr = keep_chr, genome_build = "hg19", bin_size = 5000,         workers = 1)    testthat::expect_true(methods::is(peakfiles_rebinned2, "Matrix"))    testthat::expect_equal(dim(peakfiles_rebinned2), c(416959,         2))})
34: eval(code, test_env)
35: eval(code, test_env)
36: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
42: tryCatchList(expr, classes, parentenv, handlers)
43: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
44: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
45: source_file(path, env = env(env), desc = desc, error_call = error_call)
46: FUN(X[[i]], ...)
47: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
48: doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
50: tryCatchList(expr, classes, parentenv, handlers)
51: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
52: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
53: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
54: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
55: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
56: test_check("EpiCompare")
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(v, na.rm = na.rm)
 3: viewMeans(v, na.rm = na.rm)
 4: viewMeans2(v, na.rm = na.rm)
 5: FUN(X[[i]], ...)
 6: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 7: lapply(names(numvar), function(seqname) {    v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]])    viewMeans2(v, na.rm = na.rm)})
 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,     varname = "score", na.rm = FALSE)
 9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: apply_fun(FUN = FUN, X, ...)
20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) {    gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols,         initial_threshold = 0)    gr_names <- names(GenomicRanges::mcols(gr))    intens_col <- gr_names[gr_names %in% paste(intensity_cols,         "percentile", sep = "_")][1]    data_cov <- GenomicRanges::coverage(gr, weight = intens_col)    rm(gr)    gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov,         varname = "score", na.rm = FALSE)    return(gr$score)}, ...)
21: EpiCompare::rebin_peaks(peakfiles = peakfiles, genome_build = "hg19",     bin_size = 5000, workers = 1)
22: eval(code, test_env)
23: eval(code, test_env)
24: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
32: test_code(desc, code, env = parent.frame(), reporter = reporter)
33: test_that("rebin_peaks works", {    data("CnR_H3K27ac")    data("CnT_H3K27ac")    peakfiles <- list(CnR_H3K27ac = CnR_H3K27ac, CnT_H3K27ac = CnT_H3K27ac,         CnT_missing = CnT_H3K27ac)    GenomicRanges::mcols(peakfiles$CnT_missing)$qValue <- NULL    GenomicRanges::mcols(peakfiles$CnT_missing)$score <- NULL    peakfiles_rebinned <- EpiCompare::rebin_peaks(peakfiles = peakfiles,         genome_build = "hg19", bin_size = 5000, workers = 1)    testthat::expect_true(methods::is(peakfiles_rebinned, "Matrix"))    testthat::expect_equal(dim(peakfiles_rebinned), c(647114,         2))    keep_chr <- paste0("chr", seq_len(12))    peakfiles_rebinned2 <- EpiCompare::rebin_peaks(peakfiles = peakfiles,         keep_chr = keep_chr, genome_build = "hg19", bin_size = 5000,         workers = 1)    testthat::expect_true(methods::is(peakfiles_rebinned2, "Matrix"))    testthat::expect_equal(dim(peakfiles_rebinned2), c(416959,         2))})
34: eval(code, test_env)
35: eval(code, test_env)
36: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
42: tryCatchList(expr, classes, parentenv, handlers)
43: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
44: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
45: source_file(path, env = env(env), desc = desc, error_call = error_call)
46: FUN(X[[i]], ...)
47: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
48: doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
50: tryCatchList(expr, classes, parentenv, handlers)
51: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
52: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
53: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
54: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
55: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
56: test_check("EpiCompare")
An irrecoverable exception occurred. R is aborting now ...
Merging data into matrix.
--- Running tss_plot() ---
>> Running bootstrapping for tag matrix...		 2025-01-24 22:08:59 
>> Running bootstrapping for tag matrix...		 2025-01-24 22:08:59 
Done.
--- Running width_boxplot() ---
Done.
[ FAIL 4 | WARN 10 | SKIP 0 | PASS 77 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-EpiCompare.R:16:3'): EpiCompare works ──────────────────────────
Error in ``rownames<-`(`*tmp*`, value = paste0(GenomicRanges::seqnames(gr_windows), 
    sep[1], GenomicRanges::start(gr_windows), sep[2], GenomicRanges::end(gr_windows)))`: attempt to set 'rownames' on an object with no dimensions
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::plot_corr(...)
 30.     └─EpiCompare::compute_corr(...)
 31.       └─EpiCompare::rebin_peaks(...)
 32.         └─base::`rownames<-`(...)
── Error ('test-compute_corr.R:16:9'): compute_corr works ──────────────────────
Error in ``rownames<-`(`*tmp*`, value = paste0(GenomicRanges::seqnames(gr_windows), 
    sep[1], GenomicRanges::start(gr_windows), sep[2], GenomicRanges::end(gr_windows)))`: attempt to set 'rownames' on an object with no dimensions
Backtrace:
    ▆
 1. └─base::mapply(...) at test-compute_corr.R:13:5
 2.   └─EpiCompare (local) `<fn>`(dots[[1L]][[1L]])
 3.     └─EpiCompare::compute_corr(...) at test-compute_corr.R:16:9
 4.       └─EpiCompare::rebin_peaks(...)
 5.         └─base::`rownames<-`(...)
── Error ('test-plot_corr.R:9:5'): plot_corr works ─────────────────────────────
Error in ``rownames<-`(`*tmp*`, value = paste0(GenomicRanges::seqnames(gr_windows), 
    sep[1], GenomicRanges::start(gr_windows), sep[2], GenomicRanges::end(gr_windows)))`: attempt to set 'rownames' on an object with no dimensions
Backtrace:
    ▆
 1. └─EpiCompare::plot_corr(...) at test-plot_corr.R:9:5
 2.   └─EpiCompare::compute_corr(...)
 3.     └─EpiCompare::rebin_peaks(...)
 4.       └─base::`rownames<-`(...)
── Error ('test-rebin_peaks.R:13:5'): rebin_peaks works ────────────────────────
Error in ``rownames<-`(`*tmp*`, value = paste0(GenomicRanges::seqnames(gr_windows), 
    sep[1], GenomicRanges::start(gr_windows), sep[2], GenomicRanges::end(gr_windows)))`: attempt to set 'rownames' on an object with no dimensions
Backtrace:
    ▆
 1. └─EpiCompare::rebin_peaks(...) at test-rebin_peaks.R:13:5
 2.   └─base::`rownames<-`(...)

[ FAIL 4 | WARN 10 | SKIP 0 | PASS 77 ]
Error: Test failures
Execution halted