Running ‘testthat.R’ [19s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ICAMS)
  > 
  > test_check("ICAMS")
  
   *** caught segfault ***
  address 0x555ccc27fb18, cause 'memory not mapped'
  
  Traceback:
   1: unique.default(unlist(x))
   2: unique(unlist(x))
   3: paste(unique(unlist(x)), collapse = ",")
   4: FUN(newX[, i], ...)
   5: apply(X = .SD, MARGIN = 1, FUN = GetUniqueInformation)
   6: eval(jsub, SDenv, parent.frame())
   7: eval(jsub, SDenv, parent.frame())
   8: `[.data.table`(tmp2, , `:=`((name), apply(X = .SD, MARGIN = 1,     FUN = GetUniqueInformation)), .SDcols = name1)
   9: tmp2[, `:=`((name), apply(X = .SD, MARGIN = 1, FUN = GetUniqueInformation)),     .SDcols = name1]
  10: MakeVCFDBSdf(DBSx, vcf.dt)
  11: SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
  12: FUN(X[[i]], ...)
  13: lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
  14: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
  15: suppressWarnings(lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs,     list.of.vcfs = list.of.vcfs))
  16: SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
  17: ReadAndSplitStrelkaSBSVCFs(files, names.of.VCFs, suppress.discarded.variants.warnings)
  18: StrelkaSBSVCFFilesToCatalog(files, ref.genome, trans.ranges,     region, names.of.VCFs, return.annotated.vcfs, suppress.discarded.variants.warnings)
  19: StrelkaSBSVCFFilesToZipFile(dir, zipfile = paste0(tempdir(),     "/test.zip"), ref.genome = "hg19", trans.ranges = trans.ranges.GRCh37,     region = "genome")
  20: eval(code, test_env)
  21: eval(code, test_env)
  22: 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)
  23: doTryCatch(return(expr), name, parentenv, handler)
  24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  26: doTryCatch(return(expr), name, parentenv, handler)
  27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  28: tryCatchList(expr, classes, parentenv, handlers)
  29: 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) {    })
  30: test_code(desc, code, env = parent.frame(), reporter = reporter)
  31: test_that("StrelkaSBSVCFFilesToZipFile function with no base.filename",     {        skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))        stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5"))        dir <- "testdata/Strelka-SBS-GRCh37"        out <- StrelkaSBSVCFFilesToZipFile(dir, zipfile = paste0(tempdir(),             "/test.zip"), ref.genome = "hg19", trans.ranges = trans.ranges.GRCh37,             region = "genome")        expect_type(out, "list")        name <- grep("\\.zip$", list.files(tempdir()), value = TRUE)        expect_equal(name, "test.zip")        zip::unzip(zipfile = paste0(tempdir(), "/test.zip"),             exdir = tempdir())        name1 <- grep("\\.csv$", list.files(tempdir()), value = TRUE)        expect_equal(length(name1), 6)        name2 <- grep("\\.pdf$", list.files(tempdir()), value = TRUE)        expect_equal(length(name2), 7)        unlink(file.path(tempdir(), "test.zip"))        unlink(file.path(tempdir(), name1))        unlink(file.path(tempdir(), name2))        graphics.off()        unlink("testdata/Strelka-SBS-GRCh37/Rplots.pdf")    })
  32: eval(code, test_env)
  33: eval(code, test_env)
  34: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  35: doTryCatch(return(expr), name, parentenv, handler)
  36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  37: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  38: doTryCatch(return(expr), name, parentenv, handler)
  39: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  40: tryCatchList(expr, classes, parentenv, handlers)
  41: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  42: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  43: source_file(path, env = env(env), desc = desc, error_call = error_call)
  44: FUN(X[[i]], ...)
  45: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  46: doTryCatch(return(expr), name, parentenv, handler)
  47: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  48: tryCatchList(expr, classes, parentenv, handlers)
  49: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  50: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  51: 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)
  52: 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)
  53: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  54: test_check("ICAMS")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault