• using R Under development (unstable) (2025-02-02 r87676)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.6 (1+b1)     Debian flang-new version 19.1.6 (1+b1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘ICAMS/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ICAMS’ version ‘2.3.12’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘ICAMS’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [14s/16s] OK
• checking whether the package can be loaded with stated dependencies ... [15s/20s] OK
• checking whether the package can be unloaded cleanly ... [15s/18s] OK
• checking whether the namespace can be loaded with stated dependencies ... [15s/19s] OK
• checking whether the namespace can be unloaded cleanly ... [15s/20s] OK
• checking loading without being on the library search path ... [14s/17s] OK
• checking use of S3 registration ... 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 ... [86s/106s] OK
• checking Rd files ... [1s/2s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   AnnotateDBSVCF.Rd: BSgenome   AnnotateSBSVCF.Rd: BSgenome   GeneExpressionData.Rd: data.table   ICAMS.Rd: BSgenome   MutectVCFFilesToCatalog.Rd: BSgenome   MutectVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome   MutectVCFFilesToZipFile.Rd: BSgenome   NormalizeGenomeArg.Rd: BSgenome   PlotTransBiasGeneExp.Rd: data.table   PlotTransBiasGeneExpToPdf.Rd: data.table   StrelkaSBSVCFFilesToCatalog.Rd: BSgenome   StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome   StrelkaSBSVCFFilesToZipFile.Rd: BSgenome   VCFsToCatalogs.Rd: BSgenome   VCFsToCatalogsAndPlotToPdf.Rd: BSgenome   VCFsToDBSCatalogs.Rd: BSgenome   VCFsToSBSCatalogs.Rd: BSgenome   VCFsToZipFile.Rd: BSgenome   revc.Rd: reverseComplement Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• 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 ... [1s/2s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking examples ... [14s/16s] ERROR Running examples in ‘ICAMS-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: AnnotateDBSVCF > ### Title: Add sequence context and transcript information to an in-memory > ### DBS VCF > ### Aliases: AnnotateDBSVCF > > ### ** Examples > > file <- c(system.file("extdata/Strelka-SBS-vcf", + "Strelka.SBS.GRCh37.s1.vcf", + package = "ICAMS")) > list.of.vcfs <- ReadAndSplitStrelkaSBSVCFs(file)  *** caught segfault *** address 0x5632244fcefc, 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(file) An irrecoverable exception occurred. R is aborting now ... Segmentation fault
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [33s/29s] ERROR   Running ‘testthat.R’ [32s/28s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(ICAMS)   >   > test_check("ICAMS")       *** caught segfault ***   address 0x55cc3c345268, 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
• checking PDF version of manual ... [11s/17s] OK
• checking HTML version of manual ... [6s/11s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs, 1 NOTE