Running ‘testthat.R’ [44s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ICAMS)
  > 
  > test_check("ICAMS")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_1VCFFilesToZipFile.R:7:3): MutectVCFFilesToZipFile function with no base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::MutectVCFFilesToZipFile(...) test_1VCFFilesToZipFile.R:7:2
    2.   └─ICAMS::MutectVCFFilesToCatalog(...)
    3.     └─ICAMS::VCFsToSBSCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             └─ICAMS::AnnotateSBSVCF(...)
    8.               └─ICAMS:::AddSeqContext(...)
    9.                 ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.                 └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.                   └─BSgenome:::.local(x, ...)
   12.                     └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.                       ├─base::split(names, seqnames(names))
   14.                       └─S4Vectors::split(names, seqnames(names))
   15.                         ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                         └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                           └─S4Vectors:::.local(x, f, drop, ...)
   18.                             └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                               └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                                 └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:30:3): MutectVCFFilesToZipFile function with base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::MutectVCFFilesToZipFile(...) test_1VCFFilesToZipFile.R:30:2
    2.   └─ICAMS::MutectVCFFilesToCatalog(...)
    3.     └─ICAMS::VCFsToSBSCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             └─ICAMS::AnnotateSBSVCF(...)
    8.               └─ICAMS:::AddSeqContext(...)
    9.                 ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.                 └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.                   └─BSgenome:::.local(x, ...)
   12.                     └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.                       ├─base::split(names, seqnames(names))
   14.                       └─S4Vectors::split(names, seqnames(names))
   15.                         ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                         └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                           └─S4Vectors:::.local(x, f, drop, ...)
   18.                             └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                               └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                                 └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:56:3): StrelkaSBSVCFFilesToZipFile function with no base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaSBSVCFFilesToZipFile(...) test_1VCFFilesToZipFile.R:56:2
    2.   └─ICAMS::StrelkaSBSVCFFilesToCatalog(...)
    3.     └─ICAMS::ReadAndSplitStrelkaSBSVCFs(files, names.of.VCFs, suppress.discarded.variants.warnings)
    4.       └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    5.         ├─base::suppressWarnings(...)
    6.         │ └─base::withCallingHandlers(...)
    7.         └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    8.           └─ICAMS:::FUN(X[[i]], ...)
    9.             └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
   10.               ├─GenomicRanges::reduce(ranges)
   11.               └─GenomicRanges::reduce(ranges)
   12.                 └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   13.                   └─GenomicRanges:::deconstructGRintoRGL(...)
   14.                     ├─base::split(x_ranges, x_spaceid)
   15.                     └─S4Vectors::split(x_ranges, x_spaceid)
   16.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   18.                         └─S4Vectors:::.local(x, f, drop, ...)
   19.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   20.                             └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   21.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:81:3): StrelkaSBSVCFFilesToZipFile function with base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaSBSVCFFilesToZipFile(...) test_1VCFFilesToZipFile.R:81:2
    2.   └─ICAMS::StrelkaSBSVCFFilesToCatalog(...)
    3.     └─ICAMS::ReadAndSplitStrelkaSBSVCFs(files, names.of.VCFs, suppress.discarded.variants.warnings)
    4.       └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    5.         ├─base::suppressWarnings(...)
    6.         │ └─base::withCallingHandlers(...)
    7.         └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    8.           └─ICAMS:::FUN(X[[i]], ...)
    9.             └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
   10.               ├─GenomicRanges::reduce(ranges)
   11.               └─GenomicRanges::reduce(ranges)
   12.                 └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   13.                   └─GenomicRanges:::deconstructGRintoRGL(...)
   14.                     ├─base::split(x_ranges, x_spaceid)
   15.                     └─S4Vectors::split(x_ranges, x_spaceid)
   16.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   18.                         └─S4Vectors:::.local(x, f, drop, ...)
   19.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   20.                             └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   21.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:107:3): StrelkaIDVCFFilesToZipFile function with no base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaIDVCFFilesToZipFile(...) test_1VCFFilesToZipFile.R:107:2
    2.   └─ICAMS::StrelkaIDVCFFilesToCatalog(...)
    3.     └─ICAMS::VCFsToIDCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             ├─base::suppressWarnings(...)
    8.             │ └─base::withCallingHandlers(...)
    9.             └─ICAMS::AnnotateIDVCF(...)
   10.               ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.               └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   12.                 └─BSgenome:::.local(x, ...)
   13.                   └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   14.                     ├─base::split(names, seqnames(names))
   15.                     └─S4Vectors::split(names, seqnames(names))
   16.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   18.                         └─S4Vectors:::.local(x, f, drop, ...)
   19.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   20.                             └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   21.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:132:3): StrelkaIDVCFFilesToZipFile function with base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaIDVCFFilesToZipFile(...) test_1VCFFilesToZipFile.R:132:2
    2.   └─ICAMS::StrelkaIDVCFFilesToCatalog(...)
    3.     └─ICAMS::VCFsToIDCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             ├─base::suppressWarnings(...)
    8.             │ └─base::withCallingHandlers(...)
    9.             └─ICAMS::AnnotateIDVCF(...)
   10.               ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.               └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   12.                 └─BSgenome:::.local(x, ...)
   13.                   └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   14.                     ├─base::split(names, seqnames(names))
   15.                     └─S4Vectors::split(names, seqnames(names))
   16.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   18.                         └─S4Vectors:::.local(x, f, drop, ...)
   19.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   20.                             └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   21.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:158:3): VCFsToZipFile function for Mutect VCFs with no base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::VCFsToZipFile(...) test_1VCFFilesToZipFile.R:158:2
    2.   └─ICAMS::VCFsToCatalogs(...)
    3.     └─ICAMS::VCFsToSBSCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             └─ICAMS::AnnotateSBSVCF(...)
    8.               └─ICAMS:::AddSeqContext(...)
    9.                 ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.                 └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.                   └─BSgenome:::.local(x, ...)
   12.                     └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.                       ├─base::split(names, seqnames(names))
   14.                       └─S4Vectors::split(names, seqnames(names))
   15.                         ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                         └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                           └─S4Vectors:::.local(x, f, drop, ...)
   18.                             └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                               └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                                 └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:190:3): VCFsToZipFile function for Mutect VCFs with base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::VCFsToZipFile(...) test_1VCFFilesToZipFile.R:190:2
    2.   └─ICAMS::VCFsToCatalogs(...)
    3.     └─ICAMS::VCFsToSBSCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             └─ICAMS::AnnotateSBSVCF(...)
    8.               └─ICAMS:::AddSeqContext(...)
    9.                 ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.                 └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.                   └─BSgenome:::.local(x, ...)
   12.                     └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.                       ├─base::split(names, seqnames(names))
   14.                       └─S4Vectors::split(names, seqnames(names))
   15.                         ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                         └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                           └─S4Vectors:::.local(x, f, drop, ...)
   18.                             └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                               └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                                 └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:224:3): VCFsToZipFile function for Strelka SBS VCFs with no base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::VCFsToZipFile(...) test_1VCFFilesToZipFile.R:224:2
    2.   └─ICAMS::VCFsToCatalogs(...)
    3.     └─ICAMS::ReadAndSplitVCFs(...)
    4.       └─ICAMS:::SplitListOfVCFs(...)
    5.         ├─base::suppressWarnings(...)
    6.         │ └─base::withCallingHandlers(...)
    7.         └─parallel::mclapply(...)
    8.           └─base::lapply(X = X, FUN = FUN, ...)
    9.             └─ICAMS:::FUN(X[[i]], ...)
   10.               └─ICAMS:::SplitOneVCF(...)
   11.                 └─ICAMS:::SplitSBSVCF(...)
   12.                   ├─GenomicRanges::reduce(ranges)
   13.                   └─GenomicRanges::reduce(ranges)
   14.                     └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   15.                       └─GenomicRanges:::deconstructGRintoRGL(...)
   16.                         ├─base::split(x_ranges, x_spaceid)
   17.                         └─S4Vectors::split(x_ranges, x_spaceid)
   18.                           ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   19.                           └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   20.                             └─S4Vectors:::.local(x, f, drop, ...)
   21.                               └─IRanges:::default_splitAsList(x, f, drop = drop)
   22.                                 └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   23.                                   └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:256:3): VCFsToZipFile function for Strelka SBS VCFs with base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::VCFsToZipFile(...) test_1VCFFilesToZipFile.R:256:2
    2.   └─ICAMS::VCFsToCatalogs(...)
    3.     └─ICAMS::ReadAndSplitVCFs(...)
    4.       └─ICAMS:::SplitListOfVCFs(...)
    5.         ├─base::suppressWarnings(...)
    6.         │ └─base::withCallingHandlers(...)
    7.         └─parallel::mclapply(...)
    8.           └─base::lapply(X = X, FUN = FUN, ...)
    9.             └─ICAMS:::FUN(X[[i]], ...)
   10.               └─ICAMS:::SplitOneVCF(...)
   11.                 └─ICAMS:::SplitSBSVCF(...)
   12.                   ├─GenomicRanges::reduce(ranges)
   13.                   └─GenomicRanges::reduce(ranges)
   14.                     └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   15.                       └─GenomicRanges:::deconstructGRintoRGL(...)
   16.                         ├─base::split(x_ranges, x_spaceid)
   17.                         └─S4Vectors::split(x_ranges, x_spaceid)
   18.                           ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   19.                           └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   20.                             └─S4Vectors:::.local(x, f, drop, ...)
   21.                               └─IRanges:::default_splitAsList(x, f, drop = drop)
   22.                                 └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   23.                                   └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:290:3): VCFsToZipFile function for Strelka ID VCFs with no base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::VCFsToZipFile(...) test_1VCFFilesToZipFile.R:290:2
    2.   └─ICAMS::VCFsToCatalogs(...)
    3.     └─ICAMS::VCFsToIDCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             ├─base::suppressWarnings(...)
    8.             │ └─base::withCallingHandlers(...)
    9.             └─ICAMS::AnnotateIDVCF(...)
   10.               ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.               └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   12.                 └─BSgenome:::.local(x, ...)
   13.                   └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   14.                     ├─base::split(names, seqnames(names))
   15.                     └─S4Vectors::split(names, seqnames(names))
   16.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   18.                         └─S4Vectors:::.local(x, f, drop, ...)
   19.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   20.                             └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   21.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1VCFFilesToZipFile.R:323:3): VCFsToZipFile function for Strelka ID VCFs with base.filename ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::VCFsToZipFile(...) test_1VCFFilesToZipFile.R:323:2
    2.   └─ICAMS::VCFsToCatalogs(...)
    3.     └─ICAMS::VCFsToIDCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             ├─base::suppressWarnings(...)
    8.             │ └─base::withCallingHandlers(...)
    9.             └─ICAMS::AnnotateIDVCF(...)
   10.               ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.               └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   12.                 └─BSgenome:::.local(x, ...)
   13.                   └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   14.                     ├─base::split(names, seqnames(names))
   15.                     └─S4Vectors::split(names, seqnames(names))
   16.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   18.                         └─S4Vectors:::.local(x, f, drop, ...)
   19.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   20.                             └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   21.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1strandbias_functions.R:6:3): PlotTransBiasGeneExpToPdf function ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitStrelkaSBSVCFs("testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s1.vcf") test_1strandbias_functions.R:6:2
    2.   └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    6.       └─ICAMS:::FUN(X[[i]], ...)
    7.         └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    8.           ├─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   11.               └─GenomicRanges:::deconstructGRintoRGL(...)
   12.                 ├─base::split(x_ranges, x_spaceid)
   13.                 └─S4Vectors::split(x_ranges, x_spaceid)
   14.                   ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors:::.local(x, f, drop, ...)
   17.                       └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                         └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   19.                           └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_1strandbias_functions.R:73:3): PlotTransBiasGeneExp function ────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitStrelkaSBSVCFs("testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s1.vcf") test_1strandbias_functions.R:73:2
    2.   └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    6.       └─ICAMS:::FUN(X[[i]], ...)
    7.         └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    8.           ├─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   11.               └─GenomicRanges:::deconstructGRintoRGL(...)
   12.                 ├─base::split(x_ranges, x_spaceid)
   13.                 └─S4Vectors::split(x_ranges, x_spaceid)
   14.                   ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors:::.local(x, f, drop, ...)
   17.                       └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                         └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   19.                           └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_AddSeqContext.R:7:3): AddSeqContext for GRCh37 ──────────────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitStrelkaSBSVCFs("testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s1.vcf") test_AddSeqContext.R:7:2
    2.   └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    6.       └─ICAMS:::FUN(X[[i]], ...)
    7.         └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    8.           ├─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   11.               └─GenomicRanges:::deconstructGRintoRGL(...)
   12.                 ├─base::split(x_ranges, x_spaceid)
   13.                 └─S4Vectors::split(x_ranges, x_spaceid)
   14.                   ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors:::.local(x, f, drop, ...)
   17.                       └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                         └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   19.                           └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_AddSeqContext.R:25:3): AddSeqContext for GRCh38 ─────────────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitStrelkaSBSVCFs("testdata/Strelka.SBS.GRCh38.vcf") test_AddSeqContext.R:25:2
    2.   └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    6.       └─ICAMS:::FUN(X[[i]], ...)
    7.         └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    8.           ├─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   11.               └─GenomicRanges:::deconstructGRintoRGL(...)
   12.                 ├─base::split(x_ranges, x_spaceid)
   13.                 └─S4Vectors::split(x_ranges, x_spaceid)
   14.                   ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors:::.local(x, f, drop, ...)
   17.                       └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                         └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   19.                           └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_AddSeqContext.R:41:3): AddSeqContext for GRCm38 ─────────────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitStrelkaSBSVCFs("testdata/Strelka.SBS.GRCm38.vcf") test_AddSeqContext.R:41:2
    2.   └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    6.       └─ICAMS:::FUN(X[[i]], ...)
    7.         └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    8.           ├─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   11.               └─GenomicRanges:::deconstructGRintoRGL(...)
   12.                 ├─base::split(x_ranges, x_spaceid)
   13.                 └─S4Vectors::split(x_ranges, x_spaceid)
   14.                   ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors:::.local(x, f, drop, ...)
   17.                       └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                         └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   19.                           └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_AnnotateIDVCF.R:8:3): AnnotateIDVCF function with hg19 ──────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::AnnotateIDVCF(id.vcf, ref.genome = BSgenome.Hsapiens.1000genomes.hs37d5::BSgenome.Hsapiens.1000genomes.hs37d5) test_AnnotateIDVCF.R:8:2
    2.   ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    3.   └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    4.     └─BSgenome:::.local(x, ...)
    5.       └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
    6.         ├─base::split(names, seqnames(names))
    7.         └─S4Vectors::split(names, seqnames(names))
    8.           ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
    9.           └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.             └─S4Vectors:::.local(x, f, drop, ...)
   11.               └─IRanges:::default_splitAsList(x, f, drop = drop)
   12.                 └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   13.                   └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_AnnotateIDVCF.R:24:3): AnnotateIDVCF with hg38 ──────────────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::AnnotateIDVCF(id.vcf, ref.genome = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38) test_AnnotateIDVCF.R:24:2
    2.   ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    3.   └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    4.     └─BSgenome:::.local(x, ...)
    5.       └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
    6.         ├─base::split(names, seqnames(names))
    7.         └─S4Vectors::split(names, seqnames(names))
    8.           ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
    9.           └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.             └─S4Vectors:::.local(x, f, drop, ...)
   11.               └─IRanges:::default_splitAsList(x, f, drop = drop)
   12.                 └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   13.                   └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_MakeCatalogFromMutectGRCh38VCF.R:6:3): MutectVCFFilesToCatalog ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::MutectVCFFilesToCatalog(...) test_MakeCatalogFromMutectGRCh38VCF.R:6:2
    2.   └─ICAMS::VCFsToSBSCatalogs(...)
    3.     └─parallel::mclapply(...)
    4.       └─base::lapply(X = X, FUN = FUN, ...)
    5.         └─ICAMS:::FUN(X[[i]], ...)
    6.           └─ICAMS::AnnotateSBSVCF(...)
    7.             └─ICAMS:::AddSeqContext(...)
    8.               ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    9.               └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.                 └─BSgenome:::.local(x, ...)
   11.                   └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   12.                     ├─base::split(names, seqnames(names))
   13.                     └─S4Vectors::split(names, seqnames(names))
   14.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                         └─S4Vectors:::.local(x, f, drop, ...)
   17.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                             └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   19.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_MakeCatalogFromStrelkaGRCh38VCF.R:6:3): StrelkaSBSVCFFilesToCatalog ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaSBSVCFFilesToCatalog(...) test_MakeCatalogFromStrelkaGRCh38VCF.R:6:2
    2.   └─ICAMS::ReadAndSplitStrelkaSBSVCFs(files, names.of.VCFs, suppress.discarded.variants.warnings)
    3.     └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    4.       ├─base::suppressWarnings(...)
    5.       │ └─base::withCallingHandlers(...)
    6.       └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    7.         └─ICAMS:::FUN(X[[i]], ...)
    8.           └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    9.             ├─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges::reduce(ranges)
   11.               └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   12.                 └─GenomicRanges:::deconstructGRintoRGL(...)
   13.                   ├─base::split(x_ranges, x_spaceid)
   14.                   └─S4Vectors::split(x_ranges, x_spaceid)
   15.                     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors:::.local(x, f, drop, ...)
   18.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                           └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   20.                             └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_MakeCatalogFromStrelkaGRCh38VCF.R:39:3): StrelkaIDVCFFilesToCatalog ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaIDVCFFilesToCatalog(...) test_MakeCatalogFromStrelkaGRCh38VCF.R:39:2
    2.   └─ICAMS::VCFsToIDCatalogs(...)
    3.     └─parallel::mclapply(...)
    4.       └─base::lapply(X = X, FUN = FUN, ...)
    5.         └─ICAMS:::FUN(X[[i]], ...)
    6.           ├─base::suppressWarnings(...)
    7.           │ └─base::withCallingHandlers(...)
    8.           └─ICAMS::AnnotateIDVCF(...)
    9.             ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.             └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.               └─BSgenome:::.local(x, ...)
   12.                 └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.                   ├─base::split(names, seqnames(names))
   14.                   └─S4Vectors::split(names, seqnames(names))
   15.                     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors:::.local(x, f, drop, ...)
   18.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                           └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                             └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_Read_and_Split_VCFs.R:17:3): Test ReadStrelkaSBSVCFs and SplitListOfStrelkaSBSVCFs ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS:::SplitListOfStrelkaSBSVCFs(vcfs) test_Read_and_Split_VCFs.R:17:2
    2.   ├─base::suppressWarnings(...)
    3.   │ └─base::withCallingHandlers(...)
    4.   └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    5.     └─ICAMS:::FUN(X[[i]], ...)
    6.       └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    7.         ├─GenomicRanges::reduce(ranges)
    8.         └─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   10.             └─GenomicRanges:::deconstructGRintoRGL(...)
   11.               ├─base::split(x_ranges, x_spaceid)
   12.               └─S4Vectors::split(x_ranges, x_spaceid)
   13.                 ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   14.                 └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors:::.local(x, f, drop, ...)
   16.                     └─IRanges:::default_splitAsList(x, f, drop = drop)
   17.                       └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   18.                         └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_Read_and_Split_VCFs.R:50:3): Test ReadAndSplitVCFs for Strelka SBS VCFs ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitStrelkaSBSVCFs(file1) test_Read_and_Split_VCFs.R:50:2
    2.   └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    6.       └─ICAMS:::FUN(X[[i]], ...)
    7.         └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    8.           ├─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   11.               └─GenomicRanges:::deconstructGRintoRGL(...)
   12.                 ├─base::split(x_ranges, x_spaceid)
   13.                 └─S4Vectors::split(x_ranges, x_spaceid)
   14.                   ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors:::.local(x, f, drop, ...)
   17.                       └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                         └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   19.                           └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_SplitStrelkaVCF.R:6:3): StrelkaSBSVCFFilesToCatalog ─────────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─testthat::expect_warning(SplitStrelkaSBSVCF(vcf[[1]])) test_SplitStrelkaVCF.R:6:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ICAMS:::SplitStrelkaSBSVCF(vcf[[1]])
    7.   ├─GenomicRanges::reduce(ranges)
    8.   └─GenomicRanges::reduce(ranges)
    9.     └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   10.       └─GenomicRanges:::deconstructGRintoRGL(...)
   11.         ├─base::split(x_ranges, x_spaceid)
   12.         └─S4Vectors::split(x_ranges, x_spaceid)
   13.           ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   14.           └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.             └─S4Vectors:::.local(x, f, drop, ...)
   16.               └─IRanges:::default_splitAsList(x, f, drop = drop)
   17.                 └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   18.                   └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_VCF_variant_caller_unknown.R:12:3): Test processing VCF with unknown variant caller ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitVCFs(...) test_VCF_variant_caller_unknown.R:12:2
    2.   └─ICAMS:::SplitListOfVCFs(...)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─parallel::mclapply(...)
    6.       └─base::lapply(X = X, FUN = FUN, ...)
    7.         └─ICAMS:::FUN(X[[i]], ...)
    8.           └─ICAMS:::SplitOneVCF(...)
    9.             └─ICAMS:::SplitSBSVCF(...)
   10.               ├─GenomicRanges::reduce(ranges)
   11.               └─GenomicRanges::reduce(ranges)
   12.                 └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   13.                   └─GenomicRanges:::deconstructGRintoRGL(...)
   14.                     ├─base::split(x_ranges, x_spaceid)
   15.                     └─S4Vectors::split(x_ranges, x_spaceid)
   16.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   18.                         └─S4Vectors:::.local(x, f, drop, ...)
   19.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   20.                             └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   21.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_VCFsToCatalogAndPlotToPdf.R:7:3): CatalogAndPlotToPdf function for Mutect VCFs ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::VCFsToCatalogsAndPlotToPdf(...) test_VCFsToCatalogAndPlotToPdf.R:7:2
    2.   └─ICAMS::VCFsToCatalogs(...)
    3.     └─ICAMS::VCFsToSBSCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             └─ICAMS::AnnotateSBSVCF(...)
    8.               └─ICAMS:::AddSeqContext(...)
    9.                 ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.                 └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.                   └─BSgenome:::.local(x, ...)
   12.                     └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.                       ├─base::split(names, seqnames(names))
   14.                       └─S4Vectors::split(names, seqnames(names))
   15.                         ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                         └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                           └─S4Vectors:::.local(x, f, drop, ...)
   18.                             └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                               └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                                 └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_VCFsToCatalogAndPlotToPdf.R:21:3): CatalogAndPlotToPdf function for Strelka SBS VCFs ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::VCFsToCatalogsAndPlotToPdf(...) test_VCFsToCatalogAndPlotToPdf.R:21:2
    2.   └─ICAMS::VCFsToCatalogs(...)
    3.     └─ICAMS::ReadAndSplitVCFs(...)
    4.       └─ICAMS:::SplitListOfVCFs(...)
    5.         ├─base::suppressWarnings(...)
    6.         │ └─base::withCallingHandlers(...)
    7.         └─parallel::mclapply(...)
    8.           └─base::lapply(X = X, FUN = FUN, ...)
    9.             └─ICAMS:::FUN(X[[i]], ...)
   10.               └─ICAMS:::SplitOneVCF(...)
   11.                 └─ICAMS:::SplitSBSVCF(...)
   12.                   ├─GenomicRanges::reduce(ranges)
   13.                   └─GenomicRanges::reduce(ranges)
   14.                     └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   15.                       └─GenomicRanges:::deconstructGRintoRGL(...)
   16.                         ├─base::split(x_ranges, x_spaceid)
   17.                         └─S4Vectors::split(x_ranges, x_spaceid)
   18.                           ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   19.                           └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   20.                             └─S4Vectors:::.local(x, f, drop, ...)
   21.                               └─IRanges:::default_splitAsList(x, f, drop = drop)
   22.                                 └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   23.                                   └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_VCFsToCatalogAndPlotToPdf.R:35:3): CatalogAndPlotToPdf function for Strelka ID VCFs ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::VCFsToCatalogsAndPlotToPdf(...) test_VCFsToCatalogAndPlotToPdf.R:35:2
    2.   └─ICAMS::VCFsToCatalogs(...)
    3.     └─ICAMS::VCFsToIDCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             ├─base::suppressWarnings(...)
    8.             │ └─base::withCallingHandlers(...)
    9.             └─ICAMS::AnnotateIDVCF(...)
   10.               ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.               └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   12.                 └─BSgenome:::.local(x, ...)
   13.                   └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   14.                     ├─base::split(names, seqnames(names))
   15.                     └─S4Vectors::split(names, seqnames(names))
   16.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   18.                         └─S4Vectors:::.local(x, f, drop, ...)
   19.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   20.                             └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   21.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_VCFsToCatalogs.R:7:3): VCFsToCatalogs function for Mutect VCFs ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::MutectVCFFilesToCatalog(files, ref.genome = "hg19", region = "genome") test_VCFsToCatalogs.R:7:2
    2.   └─ICAMS::VCFsToSBSCatalogs(...)
    3.     └─parallel::mclapply(...)
    4.       └─base::lapply(X = X, FUN = FUN, ...)
    5.         └─ICAMS:::FUN(X[[i]], ...)
    6.           └─ICAMS::AnnotateSBSVCF(...)
    7.             └─ICAMS:::AddSeqContext(...)
    8.               ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    9.               └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.                 └─BSgenome:::.local(x, ...)
   11.                   └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   12.                     ├─base::split(names, seqnames(names))
   13.                     └─S4Vectors::split(names, seqnames(names))
   14.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                         └─S4Vectors:::.local(x, f, drop, ...)
   17.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                             └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   19.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_VCFsToCatalogs.R:32:3): VCFsToCatalogs function for Strelka SBS VCFs ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaSBSVCFFilesToCatalog(...) test_VCFsToCatalogs.R:32:2
    2.   └─ICAMS::ReadAndSplitStrelkaSBSVCFs(files, names.of.VCFs, suppress.discarded.variants.warnings)
    3.     └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    4.       ├─base::suppressWarnings(...)
    5.       │ └─base::withCallingHandlers(...)
    6.       └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    7.         └─ICAMS:::FUN(X[[i]], ...)
    8.           └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    9.             ├─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges::reduce(ranges)
   11.               └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   12.                 └─GenomicRanges:::deconstructGRintoRGL(...)
   13.                   ├─base::split(x_ranges, x_spaceid)
   14.                   └─S4Vectors::split(x_ranges, x_spaceid)
   15.                     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors:::.local(x, f, drop, ...)
   18.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                           └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   20.                             └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_VCFsToCatalogs.R:61:3): VCFsToCatalogs function for Strelka ID VCFs ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaIDVCFFilesToCatalog(...) test_VCFsToCatalogs.R:61:2
    2.   └─ICAMS::VCFsToIDCatalogs(...)
    3.     └─parallel::mclapply(...)
    4.       └─base::lapply(X = X, FUN = FUN, ...)
    5.         └─ICAMS:::FUN(X[[i]], ...)
    6.           ├─base::suppressWarnings(...)
    7.           │ └─base::withCallingHandlers(...)
    8.           └─ICAMS::AnnotateIDVCF(...)
    9.             ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.             └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.               └─BSgenome:::.local(x, ...)
   12.                 └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.                   ├─base::split(names, seqnames(names))
   14.                   └─S4Vectors::split(names, seqnames(names))
   15.                     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors:::.local(x, f, drop, ...)
   18.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                           └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                             └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_discarded_variants.R:17:3): ReadAndSplitMutectVCFs ──────────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─testthat::expect_warning(...) test_discarded_variants.R:17:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ICAMS::VCFsToSBSCatalogs(...)
    7.   └─parallel::mclapply(...)
    8.     └─base::lapply(X = X, FUN = FUN, ...)
    9.       └─ICAMS:::FUN(X[[i]], ...)
   10.         └─ICAMS::AnnotateSBSVCF(...)
   11.           └─ICAMS:::AddSeqContext(...)
   12.             ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   13.             └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   14.               └─BSgenome:::.local(x, ...)
   15.                 └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   16.                   ├─base::split(names, seqnames(names))
   17.                   └─S4Vectors::split(names, seqnames(names))
   18.                     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   19.                     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   20.                       └─S4Vectors:::.local(x, f, drop, ...)
   21.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   22.                           └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   23.                             └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_discarded_variants.R:46:3): ReadAndSplitStrelkaSBSVCFs ──────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitStrelkaSBSVCFs(files1) test_discarded_variants.R:46:2
    2.   └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    6.       └─ICAMS:::FUN(X[[i]], ...)
    7.         └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    8.           ├─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   11.               └─GenomicRanges:::deconstructGRintoRGL(...)
   12.                 ├─base::split(x_ranges, x_spaceid)
   13.                 └─S4Vectors::split(x_ranges, x_spaceid)
   14.                   ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors:::.local(x, f, drop, ...)
   17.                       └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                         └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   19.                           └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_discarded_variants.R:73:3): MutectVCFFilesToCatalog and VCFsToCatalog ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::MutectVCFFilesToCatalog(files, ref.genome = "hg19", region = "genome") test_discarded_variants.R:73:2
    2.   └─ICAMS::VCFsToSBSCatalogs(...)
    3.     └─parallel::mclapply(...)
    4.       └─base::lapply(X = X, FUN = FUN, ...)
    5.         └─ICAMS:::FUN(X[[i]], ...)
    6.           └─ICAMS::AnnotateSBSVCF(...)
    7.             └─ICAMS:::AddSeqContext(...)
    8.               ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    9.               └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.                 └─BSgenome:::.local(x, ...)
   11.                   └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   12.                     ├─base::split(names, seqnames(names))
   13.                     └─S4Vectors::split(names, seqnames(names))
   14.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                         └─S4Vectors:::.local(x, f, drop, ...)
   17.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                             └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   19.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_discarded_variants.R:96:3): StrelkaSBSVCFFilesToCatalog ─────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaSBSVCFFilesToCatalog(...) test_discarded_variants.R:96:2
    2.   └─ICAMS::ReadAndSplitStrelkaSBSVCFs(files, names.of.VCFs, suppress.discarded.variants.warnings)
    3.     └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    4.       ├─base::suppressWarnings(...)
    5.       │ └─base::withCallingHandlers(...)
    6.       └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    7.         └─ICAMS:::FUN(X[[i]], ...)
    8.           └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    9.             ├─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges::reduce(ranges)
   11.               └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   12.                 └─GenomicRanges:::deconstructGRintoRGL(...)
   13.                   ├─base::split(x_ranges, x_spaceid)
   14.                   └─S4Vectors::split(x_ranges, x_spaceid)
   15.                     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors:::.local(x, f, drop, ...)
   18.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                           └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   20.                             └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_discarded_variants.R:121:3): StrelkaIDVCFFilesToCatalog ─────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaIDVCFFilesToCatalog(...) test_discarded_variants.R:121:2
    2.   └─ICAMS::VCFsToIDCatalogs(...)
    3.     └─parallel::mclapply(...)
    4.       └─base::lapply(X = X, FUN = FUN, ...)
    5.         └─ICAMS:::FUN(X[[i]], ...)
    6.           ├─base::suppressWarnings(...)
    7.           │ └─base::withCallingHandlers(...)
    8.           └─ICAMS::AnnotateIDVCF(...)
    9.             ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.             └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.               └─BSgenome:::.local(x, ...)
   12.                 └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.                   ├─base::split(names, seqnames(names))
   14.                   └─S4Vectors::split(names, seqnames(names))
   15.                     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors:::.local(x, f, drop, ...)
   18.                         └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                           └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                             └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_extended_seq.context_functions.R:8:3): extended seq.context functions for Mutect GRCh38 vcf ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS:::CreateOnePPMFromSBSVCF(...) test_extended_seq.context_functions.R:8:2
    2.   └─ICAMS:::AddSeqContext(vcf, ref.genome = ref.genome, seq.context.width = seq.context.width)
    3.     ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    4.     └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    5.       └─BSgenome:::.local(x, ...)
    6.         └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
    7.           ├─base::split(names, seqnames(names))
    8.           └─S4Vectors::split(names, seqnames(names))
    9.             ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.             └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.               └─S4Vectors:::.local(x, f, drop, ...)
   12.                 └─IRanges:::default_splitAsList(x, f, drop = drop)
   13.                   └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   14.                     └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_extended_seq.context_functions.R:25:3): extended seq.context functions for Mutect GRCh37 vcf ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS:::CreateOnePPMFromSBSVCF(...) test_extended_seq.context_functions.R:25:2
    2.   └─ICAMS:::AddSeqContext(vcf, ref.genome = ref.genome, seq.context.width = seq.context.width)
    3.     ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    4.     └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    5.       └─BSgenome:::.local(x, ...)
    6.         └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
    7.           ├─base::split(names, seqnames(names))
    8.           └─S4Vectors::split(names, seqnames(names))
    9.             ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.             └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.               └─S4Vectors:::.local(x, f, drop, ...)
   12.                 └─IRanges:::default_splitAsList(x, f, drop = drop)
   13.                   └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   14.                     └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_extended_seq.context_functions.R:43:3): extended seq.context functions for Mutect GRCm38 vcf ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS:::CreateOnePPMFromSBSVCF(...) test_extended_seq.context_functions.R:43:2
    2.   └─ICAMS:::AddSeqContext(vcf, ref.genome = ref.genome, seq.context.width = seq.context.width)
    3.     ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    4.     └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
    5.       └─BSgenome:::.local(x, ...)
    6.         └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
    7.           ├─base::split(names, seqnames(names))
    8.           └─S4Vectors::split(names, seqnames(names))
    9.             ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.             └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.               └─S4Vectors:::.local(x, f, drop, ...)
   12.                 └─IRanges:::default_splitAsList(x, f, drop = drop)
   13.                   └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   14.                     └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_extended_seq.context_functions.R:58:3): extended seq.context functions for Strelka GRCh38 vcf ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitStrelkaSBSVCFs("testdata/Strelka.SBS.GRCh38.vcf") test_extended_seq.context_functions.R:58:2
    2.   └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    6.       └─ICAMS:::FUN(X[[i]], ...)
    7.         └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    8.           ├─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   11.               └─GenomicRanges:::deconstructGRintoRGL(...)
   12.                 ├─base::split(x_ranges, x_spaceid)
   13.                 └─S4Vectors::split(x_ranges, x_spaceid)
   14.                   ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors:::.local(x, f, drop, ...)
   17.                       └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                         └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   19.                           └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_extended_seq.context_functions.R:75:3): extended seq.context functions for Strelka GRCh37 vcf ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitStrelkaSBSVCFs("testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s1.vcf") test_extended_seq.context_functions.R:75:2
    2.   └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    6.       └─ICAMS:::FUN(X[[i]], ...)
    7.         └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    8.           ├─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   11.               └─GenomicRanges:::deconstructGRintoRGL(...)
   12.                 ├─base::split(x_ranges, x_spaceid)
   13.                 └─S4Vectors::split(x_ranges, x_spaceid)
   14.                   ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors:::.local(x, f, drop, ...)
   17.                       └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                         └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   19.                           └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_extended_seq.context_functions.R:92:3): extended seq.context functions for Strelka GRCm38 vcf ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::ReadAndSplitStrelkaSBSVCFs("testdata/Strelka.SBS.GRCm38.vcf") test_extended_seq.context_functions.R:92:2
    2.   └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    6.       └─ICAMS:::FUN(X[[i]], ...)
    7.         └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
    8.           ├─GenomicRanges::reduce(ranges)
    9.           └─GenomicRanges::reduce(ranges)
   10.             └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   11.               └─GenomicRanges:::deconstructGRintoRGL(...)
   12.                 ├─base::split(x_ranges, x_spaceid)
   13.                 └─S4Vectors::split(x_ranges, x_spaceid)
   14.                   ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   15.                   └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                     └─S4Vectors:::.local(x, f, drop, ...)
   17.                       └─IRanges:::default_splitAsList(x, f, drop = drop)
   18.                         └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   19.                           └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_parallel_computing.R:16:3): Test parallel computing for Strelka ID VCFs ──
  Error: mode(object) == "numeric" is not TRUE
  Backtrace:
      █
   1. └─ICAMS::VCFsToIDCatalogs(...) test_parallel_computing.R:16:2
   2.   └─ICAMS::as.catalog(...)
   3.     └─base::stopifnot(mode(object) == "numeric")
  ── Error (test_parallel_computing.R:52:3): Test parallel computing for Strelka SBS VCFs ──
  Error: $ operator is invalid for atomic vectors
  Backtrace:
      █
   1. └─ICAMS:::SplitListOfVCFs(...) test_parallel_computing.R:52:2
   2.   └─base::lapply(v1, function(x) x$SBS)
   3.     └─ICAMS:::FUN(X[[i]], ...)
  ── Error (test_parallel_computing.R:92:3): Test parallel computing for Mutect VCFs ──
  Error: subscript out of bounds
  Backtrace:
      █
   1. └─ICAMS::VCFsToSBSCatalogs(...) test_parallel_computing.R:92:2
   2.   └─base::lapply(list0, FUN = "[[", 2)
  ── Error (test_processing_empty_vcfs.R:43:3): Processing empty Strelka SBS vcfs ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaSBSVCFFilesToZipFile(...) test_processing_empty_vcfs.R:43:2
    2.   └─ICAMS::StrelkaSBSVCFFilesToCatalog(...)
    3.     └─ICAMS::ReadAndSplitStrelkaSBSVCFs(files, names.of.VCFs, suppress.discarded.variants.warnings)
    4.       └─ICAMS:::SplitListOfStrelkaSBSVCFs(list.of.vcfs = vcfs, suppress.discarded.variants.warnings = suppress.discarded.variants.warnings)
    5.         ├─base::suppressWarnings(...)
    6.         │ └─base::withCallingHandlers(...)
    7.         └─base::lapply(1:num.of.vcfs, GetSplitStrelkaSBSVCFs, list.of.vcfs = list.of.vcfs)
    8.           └─ICAMS:::FUN(X[[i]], ...)
    9.             └─ICAMS:::SplitStrelkaSBSVCF(list.of.vcfs[[idx]], name.of.VCF = names(list.of.vcfs)[idx])
   10.               ├─GenomicRanges::reduce(ranges)
   11.               └─GenomicRanges::reduce(ranges)
   12.                 └─GenomicRanges:::.local(x, drop.empty.ranges, ...)
   13.                   └─GenomicRanges:::deconstructGRintoRGL(...)
   14.                     ├─base::split(x_ranges, x_spaceid)
   15.                     └─S4Vectors::split(x_ranges, x_spaceid)
   16.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   18.                         └─S4Vectors:::.local(x, f, drop, ...)
   19.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   20.                             └─IRanges:::.splitAsList_by_integer_Rle(x, f, drop)
   21.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_processing_empty_vcfs.R:77:3): Processing empty Strelka ID vcfs ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::StrelkaIDVCFFilesToZipFile(...) test_processing_empty_vcfs.R:77:2
    2.   └─ICAMS::StrelkaIDVCFFilesToCatalog(...)
    3.     └─ICAMS::VCFsToIDCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             ├─base::suppressWarnings(...)
    8.             │ └─base::withCallingHandlers(...)
    9.             └─ICAMS::AnnotateIDVCF(...)
   10.               ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.               └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   12.                 └─BSgenome:::.local(x, ...)
   13.                   └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   14.                     ├─base::split(names, seqnames(names))
   15.                     └─S4Vectors::split(names, seqnames(names))
   16.                       ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                       └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   18.                         └─S4Vectors:::.local(x, f, drop, ...)
   19.                           └─IRanges:::default_splitAsList(x, f, drop = drop)
   20.                             └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   21.                               └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_processing_empty_vcfs.R:111:3): Processing empty Mutect vcfs ────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ICAMS::MutectVCFFilesToZipFile(...) test_processing_empty_vcfs.R:111:2
    2.   └─ICAMS::MutectVCFFilesToCatalog(...)
    3.     └─ICAMS::VCFsToSBSCatalogs(...)
    4.       └─parallel::mclapply(...)
    5.         └─base::lapply(X = X, FUN = FUN, ...)
    6.           └─ICAMS:::FUN(X[[i]], ...)
    7.             └─ICAMS::AnnotateSBSVCF(...)
    8.               └─ICAMS:::AddSeqContext(...)
    9.                 ├─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   10.                 └─BSgenome::getSeq(ref.genome, Ranges, as.character = TRUE)
   11.                   └─BSgenome:::.local(x, ...)
   12.                     └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.                       ├─base::split(names, seqnames(names))
   14.                       └─S4Vectors::split(names, seqnames(names))
   15.                         ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.                         └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                           └─S4Vectors:::.local(x, f, drop, ...)
   18.                             └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                               └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                                 └─S4Vectors:::isNotSorted(f_vals)
  
  [ FAIL 49 | WARN 2 | SKIP 0 | PASS 652 ]
  Error: Test failures
  Execution halted