Last updated on 2025-01-30 16:48:25 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.3.12 | 51.83 | 831.85 | 883.68 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.3.12 | 35.23 | 302.03 | 337.26 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.3.12 | 1266.24 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.3.12 | 1318.22 | OK | |||
| r-devel-windows-x86_64 | 2.3.12 | 52.00 | 553.00 | 605.00 | NOTE | |
| r-patched-linux-x86_64 | 2.3.12 | 63.64 | 665.28 | 728.92 | OK | |
| r-release-linux-x86_64 | 2.3.12 | 45.71 | 674.39 | 720.10 | OK | |
| r-release-macos-arm64 | 2.3.12 | 181.00 | NOTE | |||
| r-release-macos-x86_64 | 2.3.12 | 286.00 | NOTE | |||
| r-release-windows-x86_64 | 2.3.12 | 52.00 | 559.00 | 611.00 | OK | |
| r-oldrel-macos-arm64 | 2.3.12 | 197.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2.3.12 | 419.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 2.3.12 | 68.00 | 527.00 | 595.00 | NOTE |
Version: 2.3.12
Check: Rd cross-references
Result: 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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 2.3.12
Check: examples
Result: 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 0x55957ef707ec, 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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.3.12
Check: tests
Result: ERROR
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.3.12
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'BSgenome.Hsapiens.1000genomes.hs37d5',
'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 2.3.12
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'BSgenome.Hsapiens.1000genomes.hs37d5',
'BSgenome.Mmusculus.UCSC.mm10'
Flavor: r-oldrel-windows-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.