Issue with maftools::gtMarkers memory not mapped

[grantn5]

Describe the issue There is an issue with gtMarkers and the underlying C code of how the function is executed. This results in an error of

*** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
 2: suppressWarnings(invisible(.Call("snpc", b, lfile, mapq, sam_flag,     fa, opcount, PACKAGE = "maftools")))
 3: withCallingHandlers(suppressWarnings(invisible(.Call("snpc",     b, lfile, mapq, sam_flag, fa, opcount, PACKAGE = "maftools"))))
 4: FUN(X[[i]], ...)
 5: lapply(X = X, FUN = FUN, ...)
 6: parallel::mclapply(loci_files, function(lfile) {    chr = unlist(data.table::tstrsplit(basename(path = lfile),         split = "_", keep = 1))    if (verbose) {        system(paste("echo ' current chromosome:", chr, "'"))    }    opcount = tempfile(pattern = paste0(chr, "_", basename(b)),         fileext = ".tsv")    withCallingHandlers(suppressWarnings(invisible(.Call("snpc",         b, lfile, mapq, sam_flag, fa, opcount, PACKAGE = "maftools"))))    paste0(opcount, ".tsv")}, mc.cores = nthreads)
 7: maftools::gtMarkers(t_bam = "processed_data/PDM-132/PDM-132.recal.bam",     build = "hg38", fa = "processed_data/references/Homo_sapiens_assembly38.fasta",     nthreads = 1, verbose = TRUE)

To make sure I have got all the correct libraries installed with no conflicts I pulled the docker form biocontainers and ran the command within the image

docker pull quay.io/biocontainers/bioconductor-maftools:2.18.0--r43ha9d7317_1

This container does not contain the R.utils library so needs to be installed i then ran the following command

Command Please post your commands and the output (errors or any unexpected output)

maftools::gtMarkers(t_bam = "my_tumor.bam", ##No test bam so can't make reprex
                             build = "hg38",
                             nthreads = 1, 
                             verbose = TRUE
                            )

Which will give the error.

Session info Run sessionInfo() and post the output below

sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.27.so;  LAPACK version 3.12.0

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: NA
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_4.3.3     Matrix_1.6-5       DNAcopy_1.76.0     parallel_4.3.3    
 [5] tools_4.3.3        RColorBrewer_1.1-3 survival_3.6-4     R.methodsS3_1.8.2 
 [9] splines_4.3.3      grid_4.3.3         data.table_1.15.2  maftools_2.18.0   
[13] R.utils_2.12.3     R.oo_1.26.0        lattice_0.22-6 

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