Running ‘testthat.R’ [80s/115s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ICAMS)
  > 
  > test_check("ICAMS")
  
   *** caught segfault ***
  address 0xfffffffecc7e1d8c, 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("testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s1.vcf")
  18: eval(code, test_env)
  19: eval(code, test_env)
  20: 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)
  21: doTryCatch(return(expr), name, parentenv, handler)
  22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  23: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  24: doTryCatch(return(expr), name, parentenv, handler)
  25: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  26: tryCatchList(expr, classes, parentenv, handlers)
  27: 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) {    })
  28: test_code(desc, code, env = parent.frame(), reporter = reporter)
  29: test_that("PlotTransBiasGeneExp function", {    skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))    stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5"))    list.of.vcfs <- ReadAndSplitStrelkaSBSVCFs("testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s1.vcf")    annotated.SBS.vcf <- AnnotateSBSVCF(list.of.vcfs$SBS.vcfs[[1]],         "hg19", trans.ranges.GRCh37)    vcf1 <- annotated.SBS.vcf[REF == "C", ]    vcf2 <- annotated.SBS.vcf[REF %in% c("C", "G"), ]    vcf3 <- annotated.SBS.vcf[REF == "T", ]    vcf4 <- annotated.SBS.vcf[REF %in% c("A", "T"), ]    out <- PlotTransBiasGeneExp(annotated.SBS.vcf = annotated.SBS.vcf,         expression.data = gene.expression.data.HepG2, Ensembl.gene.ID.col = "Ensembl.gene.ID",         expression.value.col = "TPM", num.of.bins = 4, plot.type = "C>A")    out1 <- PlotTransBiasGeneExp(annotated.SBS.vcf = vcf1, expression.data = gene.expression.data.HepG2,         Ensembl.gene.ID.col = "Ensembl.gene.ID", expression.value.col = "TPM",         num.of.bins = 4, plot.type = "C>A")    out2 <- PlotTransBiasGeneExp(annotated.SBS.vcf = vcf2, expression.data = gene.expression.data.HepG2,         Ensembl.gene.ID.col = "Ensembl.gene.ID", expression.value.col = "TPM",         num.of.bins = 4, plot.type = "C>A")    out3 <- PlotTransBiasGeneExp(annotated.SBS.vcf = vcf3, expression.data = gene.expression.data.HepG2,         Ensembl.gene.ID.col = "Ensembl.gene.ID", expression.value.col = "TPM",         num.of.bins = 4, plot.type = "C>A")    out4 <- PlotTransBiasGeneExp(annotated.SBS.vcf = vcf4, expression.data = gene.expression.data.HepG2,         Ensembl.gene.ID.col = "Ensembl.gene.ID", expression.value.col = "TPM",         num.of.bins = 4, plot.type = "C>A")    expect_equal(out$plot.success, TRUE)    expect_equal(out1$plot.success, TRUE)    expect_equal(out2$plot.success, TRUE)    expect_equal(out3$plot.success, TRUE)    expect_equal(out4$plot.success, TRUE)    graphics.off()})
  30: eval(code, test_env)
  31: eval(code, test_env)
  32: 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)
  33: doTryCatch(return(expr), name, parentenv, handler)
  34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  35: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  36: doTryCatch(return(expr), name, parentenv, handler)
  37: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  38: tryCatchList(expr, classes, parentenv, handlers)
  39: 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) {    })
  40: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  41: source_file(path, env = env(env), desc = desc, error_call = error_call)
  42: FUN(X[[i]], ...)
  43: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  44: doTryCatch(return(expr), name, parentenv, handler)
  45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  46: tryCatchList(expr, classes, parentenv, handlers)
  47: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  48: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  49: 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)
  50: 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)
  51: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  52: test_check("ICAMS")
  An irrecoverable exception occurred. R is aborting now ...