rebin_peaks: Segfault (memory not mapped) for R-devel v4.5.0

[HDash]

1. Bug description

All functions which call for rebin_peaks fail under R-devel v4.5.0 (tested with 2025-01-19 r87600 and prior). Everything works as expected with the latest R-release.

2. Reproducible example

Running example for rebin_peaks

devtools::load_all()
#> ℹ Loading EpiCompare
#> Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern'
#> when loading 'genomation'

data("CnR_H3K27ac") 
data("CnT_H3K27ac")
peakfiles <- list(CnR_H3K27ac=CnR_H3K27ac, CnT_H3K27ac=CnT_H3K27ac) 

peakfiles_rebinned <- rebin_peaks(peakfiles = peakfiles,
                                 genome_build = "hg19",
                                  bin_size = 5000,
                                 workers = 1)
#> Standardising peak files in 647,114 bins of 5,000 bp.
#> 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 = c("chr1:1-5000", "chr1:5001-10000", : attempt to set 'rownames' on an object with no dimensions

^{Created on 2025-01-20 with reprex v2.1.1}

Data

(Built-in)

3. Session info

utils::sessionInfo()
#> R Under development (unstable) (2025-01-19 r87600)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.5 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/hd423/downloads/R-devel/lib/libRblas.so 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0  LAPACK version 3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] compiler_4.5.0    fastmap_1.2.0     cli_3.6.3         tools_4.5.0      
#>  [5] htmltools_0.5.8.1 withr_3.0.2       fs_1.6.5          glue_1.8.0       
#>  [9] yaml_2.3.10       rmarkdown_2.29    knitr_1.49        reprex_2.1.1     
#> [13] xfun_0.50         digest_0.6.37     lifecycle_1.0.4   rlang_1.1.5      
#> [17] evaluate_1.0.3

^{Created on 2025-01-20 with reprex v2.1.1}

[HDash]

Traceback

 *** 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 = peakfiles, genome_build = "hg19", bin_size = 5000,     workers = 1)

[HDash]

Issue persists with past commit c2719d6, which previously passed all checks on push.

[HDash]

Segfault somewhere here

https://github.com/Bioconductor/IRanges/blob/4eff83a94e30320f225dacdea9654d37b623e99f/src/RleViews_utils.c#L377-L560

C code for ViewMeans() from IRanges package. However, this code has not been modified in over years.