Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ICAMS)
  Warning message:
  multiple methods tables found for 'export' 
  > 
  > test_check("ICAMS")
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Mmusculus.UCSC.mm10', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Mmusculus.UCSC.mm10', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Mmusculus.UCSC.mm10', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Mmusculus.UCSC.mm10', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Mmusculus.UCSC.mm10', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  Failed with error:  '.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.1000genomes.hs37d5', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")'
  == Failed tests ================================================================
  -- Error (test_0TransformCatalogDBS144.R:5:3): Transformation of a DBS 144 catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_0TransformCatalogDBS144.R:5:2
  -- Error (test_0TransformCatalogSBS192.R:5:3): Transformation of a SBS 192 catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_0TransformCatalogSBS192.R:5:2
  -- Error (test_1TransformCatalog.R:7:3): Legal transformation 1;
  counts -> counts; genome counts -> exome counts,
  and exome counts -> genome counts --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:7:2
  -- Error (test_1TransformCatalog.R:31:3): Legal transformation 2;
  counts -> density; genome counts -> density,
  and genome counts -> exome count -> density --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:31:2
  -- Error (test_1TransformCatalog.R:60:3): Legal transformation 3;
  counts -> density; genome GRCh37 counts -> genome GRCh37 density,
  and genome GRCh37 counts -> genome GRCh38 counts -> genome GRCh38 density --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:60:2
  -- Error (test_1TransformCatalog.R:90:3): Legal transformations 1, 2, and 4;
  genome GRCh37 counts -> genome GRCh38 counts,
  and genome GRCh37 counts -> genome GRCh37 density -> genome GRCh38 counts --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:90:2
  -- Error (test_1TransformCatalog.R:115:3): Legal transformation 4; density -> (genome) counts --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:115:2
  -- Error (test_1TransformCatalog.R:134:3): Legal transformation 5;
  density -> counts.signature, density -> density.signature --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:134:2
  -- Error (test_1TransformCatalog.R:160:3): Legal transformations 3 and 6;
  genome counts -> exome counts.signature,
  and genome counts.signature -> exome counts.signature --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:160:2
  -- Error (test_1TransformCatalog.R:197:3): Legal transformation 6;
  counts.signature -> density.signature,
  and genome counts -> exome counts.signature --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:197:2
  -- Error (test_1TransformCatalog.R:254:13): going from density to density,
            density.signature to density.signature --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:254:12
  -- Error (test_1TransformCatalog.R:284:15): Error test: counts.singature -> counts or density,
              error message expected --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:284:14
  -- Error (test_1TransformCatalog.R:306:13): Transform a counts catalog with NULL abundance,
            to counts.signature catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1TransformCatalog.R:306:12
  -- Error (test_1VCFFilesToZipFile.R:5:3): MutectVCFFilesToZipFile function with no base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:5:2
  -- Error (test_1VCFFilesToZipFile.R:28:3): MutectVCFFilesToZipFile function with base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:28:2
  -- Error (test_1VCFFilesToZipFile.R:54:3): StrelkaSBSVCFFilesToZipFile function with no base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:54:2
  -- Error (test_1VCFFilesToZipFile.R:79:3): StrelkaSBSVCFFilesToZipFile function with base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:79:2
  -- Error (test_1VCFFilesToZipFile.R:105:3): StrelkaIDVCFFilesToZipFile function with no base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:105:2
  -- Error (test_1VCFFilesToZipFile.R:130:3): StrelkaIDVCFFilesToZipFile function with base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:130:2
  -- Error (test_1VCFFilesToZipFile.R:156:3): VCFsToZipFile function for Mutect VCFs with no base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:156:2
  -- Error (test_1VCFFilesToZipFile.R:188:3): VCFsToZipFile function for Mutect VCFs with base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:188:2
  -- Error (test_1VCFFilesToZipFile.R:222:3): VCFsToZipFile function for Strelka SBS VCFs with no base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:222:2
  -- Error (test_1VCFFilesToZipFile.R:254:3): VCFsToZipFile function for Strelka SBS VCFs with base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:254:2
  -- Error (test_1VCFFilesToZipFile.R:288:3): VCFsToZipFile function for Strelka ID VCFs with no base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:288:2
  -- Error (test_1VCFFilesToZipFile.R:321:3): VCFsToZipFile function for Strelka ID VCFs with base.filename --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1VCFFilesToZipFile.R:321:2
  -- Error (test_1strandbias_functions.R:5:3): PlotTransBiasGeneExpToPdf function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1strandbias_functions.R:5:2
  -- Error (test_1strandbias_functions.R:72:3): PlotTransBiasGeneExp function ----
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_1strandbias_functions.R:72:2
  -- Error (test_AddSeqContext.R:5:3): AddSeqContext for GRCh37 ------------------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_AddSeqContext.R:5:2
  -- Error (test_AddSeqContext.R:23:3): AddSeqContext for GRCh38 -----------------
  Error: requireNamespace("BSgenome.Hsapiens.UCSC.hg38") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) test_AddSeqContext.R:23:2
  -- Error (test_AddSeqContext.R:39:3): AddSeqContext for GRCm38 -----------------
  Error: requireNamespace("BSgenome.Mmusculus.UCSC.mm10") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Mmusculus.UCSC.mm10")) test_AddSeqContext.R:39:2
  -- Error (test_AnnotateIDVCF.R:5:3): AnnotateIDVCF function with hg19 ----------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_AnnotateIDVCF.R:5:2
  -- Error (test_AnnotateIDVCF.R:21:3): AnnotateIDVCF with hg38 ------------------
  Error: requireNamespace("BSgenome.Hsapiens.UCSC.hg38") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) test_AnnotateIDVCF.R:21:2
  -- Error (test_CheckAndFixChrNames.R:5:3): CheckAndFixChrNames for human genome 37 --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_CheckAndFixChrNames.R:5:2
  -- Error (test_CheckAndFixChrNames.R:88:3): CheckAndFixChrNames for human genome 38 --
  Error: requireNamespace("BSgenome.Hsapiens.UCSC.hg38") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) test_CheckAndFixChrNames.R:88:2
  -- Error (test_CheckAndFixChrNames.R:170:3): CheckAndFixChrNames for mouse genome --
  Error: requireNamespace("BSgenome.Mmusculus.UCSC.mm10") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Mmusculus.UCSC.mm10")) test_CheckAndFixChrNames.R:170:2
  -- Error (test_CheckAndFixChrNamesForTransRanges.R:5:3): CheckAndFixChrNamesForTransRanges for human genome 37 --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_CheckAndFixChrNamesForTransRanges.R:5:2
  -- Error (test_CheckAndFixChrNamesForTransRanges.R:111:3): CheckAndFixChrNamesForTransRanges for human genome 38 --
  Error: requireNamespace("BSgenome.Hsapiens.UCSC.hg38") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) test_CheckAndFixChrNamesForTransRanges.R:111:2
  -- Error (test_CheckAndFixChrNamesForTransRanges.R:212:3): CheckAndFixChrNamesForTransRanges for mouse genome --
  Error: requireNamespace("BSgenome.Mmusculus.UCSC.mm10") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Mmusculus.UCSC.mm10")) test_CheckAndFixChrNamesForTransRanges.R:212:2
  -- Error (test_CollapseCatalog.R:5:3): Collapse1536CatalogTo96 block 1 ---------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_CollapseCatalog.R:5:2
  -- Error (test_CollapseCatalog.R:40:3): Collapse192CatalogTo96 block 2 ---------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_CollapseCatalog.R:40:2
  -- Error (test_CollapseCatalog.R:75:3): Collapse144CatalogTo78 -----------------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_CollapseCatalog.R:75:2
  -- Error (test_MakeCatalogFromMutectGRCh38VCF.R:5:3): MutectVCFFilesToCatalog --
  Error: requireNamespace("BSgenome.Hsapiens.UCSC.hg38") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) test_MakeCatalogFromMutectGRCh38VCF.R:5:2
  -- Error (test_MakeCatalogFromStrelkaGRCh38VCF.R:5:3): StrelkaSBSVCFFilesToCatalog --
  Error: requireNamespace("BSgenome.Hsapiens.UCSC.hg38") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) test_MakeCatalogFromStrelkaGRCh38VCF.R:5:2
  -- Error (test_MakeCatalogFromStrelkaGRCh38VCF.R:38:3): StrelkaIDVCFFilesToCatalog --
  Error: requireNamespace("BSgenome.Hsapiens.UCSC.hg38") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) test_MakeCatalogFromStrelkaGRCh38VCF.R:38:2
  -- Error (test_PlotCatalog.DBS136Catalog.R:5:3): PlotCatalog.DBS136Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalog.DBS136Catalog.R:5:2
  -- Error (test_PlotCatalog.DBS144Catalog.R:5:3): PlotCatalog.DBS144Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalog.DBS144Catalog.R:5:2
  -- Error (test_PlotCatalog.DBS78Catalog.R:5:3): PlotCatalog.DBS78Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalog.DBS78Catalog.R:5:2
  -- Error (test_PlotCatalog.IndelCatalog.R:5:3): PlotCatalog.IndelCatalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalog.IndelCatalog.R:5:2
  -- Error (test_PlotCatalog.SBS1536Catalog.R:5:3): PlotCatalog.SBS1536Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalog.SBS1536Catalog.R:5:2
  -- Error (test_PlotCatalog.SBS192Catalog.R:5:3): PlotCatalog.SBS192Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalog.SBS192Catalog.R:5:2
  -- Error (test_PlotCatalog.SBS96Catalog.R:5:3): PlotCatalog.SBS96Catalog for one column catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalog.SBS96Catalog.R:5:2
  -- Error (test_PlotCatalog.SBS96Catalog.R:93:3): PlotCatalog.SBS96Catalog for two column catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalog.SBS96Catalog.R:93:2
  -- Error (test_PlotCatalogToPdf.DBS136Catalog.R:5:3): PlotCatalogToPdf.DBS136Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalogToPdf.DBS136Catalog.R:5:2
  -- Error (test_PlotCatalogToPdf.DBS144Catalog.R:5:3): PlotCatalogToPdf.DBS144Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalogToPdf.DBS144Catalog.R:5:2
  -- Error (test_PlotCatalogToPdf.DBS78Catalog.R:5:3): PlotCatalogToPdf.DBS78Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalogToPdf.DBS78Catalog.R:5:2
  -- Error (test_PlotCatalogToPdf.IndelCatalog.R:5:3): PlotCatalogToPdf.IndelCatalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalogToPdf.IndelCatalog.R:5:2
  -- Error (test_PlotCatalogToPdf.SBS1536Catalog.R:5:3): PlotCatalogToPdf.SBS1536Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalogToPdf.SBS1536Catalog.R:5:2
  -- Error (test_PlotCatalogToPdf.SBS192Catalog.R:5:3): PlotCatalogToPdf.SBS192Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalogToPdf.SBS192Catalog.R:5:2
  -- Error (test_PlotCatalogToPdf.SBS96Catalog.R:5:3): PlotCatalogToPdf.SBS96Catalog function --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_PlotCatalogToPdf.SBS96Catalog.R:5:2
  -- Error (test_ReadCatalog.R:3:3): Functions for converting COSMIC and SigProfiler-formatted catalogs to ICAMS --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_ReadCatalog.R:3:2
  -- Error (test_ReadWriteCatalog.R:3:3): Functions for reading and writing catalogs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_ReadWriteCatalog.R:3:2
  -- Error (test_VCFsToCatalogAndPlotToPdf.R:5:3): CatalogAndPlotToPdf function for Mutect VCFs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_VCFsToCatalogAndPlotToPdf.R:5:2
  -- Error (test_VCFsToCatalogAndPlotToPdf.R:19:3): CatalogAndPlotToPdf function for Strelka SBS VCFs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_VCFsToCatalogAndPlotToPdf.R:19:2
  -- Error (test_VCFsToCatalogAndPlotToPdf.R:33:3): CatalogAndPlotToPdf function for Strelka ID VCFs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_VCFsToCatalogAndPlotToPdf.R:33:2
  -- Error (test_VCFsToCatalogs.R:5:3): VCFsToCatalogs function for Mutect VCFs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_VCFsToCatalogs.R:5:2
  -- Error (test_VCFsToCatalogs.R:30:3): VCFsToCatalogs function for Strelka SBS VCFs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_VCFsToCatalogs.R:30:2
  -- Error (test_VCFsToCatalogs.R:59:3): VCFsToCatalogs function for Strelka ID VCFs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_VCFsToCatalogs.R:59:2
  -- Error (test_cbind_catalogs.R:5:3): cbind method for SBS96Catalog ------------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_cbind_catalogs.R:5:2
  -- Error (test_cbind_catalogs.R:150:3): cbind method for SBS192Catalog ---------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_cbind_catalogs.R:150:2
  -- Error (test_cbind_catalogs.R:296:3): cbind method for SBS1536Catalog --------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_cbind_catalogs.R:296:2
  -- Error (test_cbind_catalogs.R:441:3): cbind method for DBS78Catalog ----------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_cbind_catalogs.R:441:2
  -- Error (test_cbind_catalogs.R:586:3): cbind method for DBS144Catalog ---------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_cbind_catalogs.R:586:2
  -- Error (test_cbind_catalogs.R:732:3): cbind method for DBS136Catalog ---------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_cbind_catalogs.R:732:2
  -- Error (test_cbind_catalogs.R:878:3): cbind method for IndelCatalog ----------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_cbind_catalogs.R:878:2
  -- Error (test_discarded_variants.R:5:3): ReadAndSplitMutectVCFs ---------------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_discarded_variants.R:5:2
  -- Error (test_discarded_variants.R:71:3): MutectVCFFilesToCatalog and VCFsToCatalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_discarded_variants.R:71:2
  -- Error (test_discarded_variants.R:94:3): StrelkaSBSVCFFilesToCatalog ---------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_discarded_variants.R:94:2
  -- Error (test_discarded_variants.R:119:3): StrelkaIDVCFFilesToCatalog ---------
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_discarded_variants.R:119:2
  -- Error (test_extended_seq.context_functions.R:5:3): extended seq.context functions for Mutect GRCh38 vcf --
  Error: requireNamespace("BSgenome.Hsapiens.UCSC.hg38") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) test_extended_seq.context_functions.R:5:2
  -- Error (test_extended_seq.context_functions.R:22:3): extended seq.context functions for Mutect GRCh37 vcf --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_extended_seq.context_functions.R:22:2
  -- Error (test_extended_seq.context_functions.R:39:3): extended seq.context functions for Mutect GRCm38 vcf --
  Error: requireNamespace("BSgenome.Mmusculus.UCSC.mm10") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Mmusculus.UCSC.mm10")) test_extended_seq.context_functions.R:39:2
  -- Error (test_extended_seq.context_functions.R:57:3): extended seq.context functions for Strelka GRCh38 vcf --
  Error: requireNamespace("BSgenome.Hsapiens.UCSC.hg38") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) test_extended_seq.context_functions.R:57:2
  -- Error (test_extended_seq.context_functions.R:74:3): extended seq.context functions for Strelka GRCh37 vcf --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_extended_seq.context_functions.R:74:2
  -- Error (test_extended_seq.context_functions.R:91:3): extended seq.context functions for Strelka GRCm38 vcf --
  Error: requireNamespace("BSgenome.Mmusculus.UCSC.mm10") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Mmusculus.UCSC.mm10")) test_extended_seq.context_functions.R:91:2
  -- Error (test_methods_for_subsetting_catalogs.R:5:3): [ method for SBS96Catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_methods_for_subsetting_catalogs.R:5:2
  -- Error (test_methods_for_subsetting_catalogs.R:22:3): [ method for SBS192Catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_methods_for_subsetting_catalogs.R:22:2
  -- Error (test_methods_for_subsetting_catalogs.R:40:3): [ method for SBS1536Catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_methods_for_subsetting_catalogs.R:40:2
  -- Error (test_methods_for_subsetting_catalogs.R:57:3): [ method for DBS78Catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_methods_for_subsetting_catalogs.R:57:2
  -- Error (test_methods_for_subsetting_catalogs.R:74:3): [ method for DBS144Catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_methods_for_subsetting_catalogs.R:74:2
  -- Error (test_methods_for_subsetting_catalogs.R:92:3): [ method for DBS136Catalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_methods_for_subsetting_catalogs.R:92:2
  -- Error (test_methods_for_subsetting_catalogs.R:109:3): [ method for IndelCatalog --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_methods_for_subsetting_catalogs.R:109:2
  -- Error (test_parallel_computing.R:5:3): Test parallel computing for Strelka ID VCFs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_parallel_computing.R:5:2
  -- Error (test_parallel_computing.R:40:3): Test parallel computing for Strelka SBS VCFs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_parallel_computing.R:40:2
  -- Error (test_parallel_computing.R:79:3): Test parallel computing for Mutect VCFs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_parallel_computing.R:79:2
  -- Error (test_processing_empty_vcfs.R:5:3): Processing empty Strelka SBS vcfs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_processing_empty_vcfs.R:5:2
  -- Error (test_processing_empty_vcfs.R:58:3): Processing empty Strelka ID vcfs --
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_processing_empty_vcfs.R:58:2
  -- Error (test_processing_empty_vcfs.R:92:3): Processing empty Mutect vcfs -----
  Error: requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5") is not TRUE
  Backtrace:
      x
   1. \-base::stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5")) test_processing_empty_vcfs.R:92:2
  
  [ FAIL 97 | WARN 0 | SKIP 0 | PASS 159 ]
  Error: Test failures
  Execution halted