Running ‘testthat.R’ [53s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ICAMS)
  > 
  > test_check("ICAMS")
  ── 1. Error: Transform a counts catalog with NULL abundance,
            to counts
  
  Please install BSgenome.Hsapiens.1000genomes.hs37d5:
  BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")
  Backtrace:
   1. ICAMS::ReadCatalog(...)
   2. ICAMS:::ReadCatalog.SBS96Catalog(...)
   3. ICAMS::as.catalog(out, ref.genome, region, catalog.type)
   4. ICAMS:::NormalizeGenomeArg(ref.genome)
  
  ── 2. Error: ReadAndSplitMutectVCFs (@test_discarded_variants.R#15)  ───────────
  
  Please install BSgenome.Hsapiens.1000genomes.hs37d5:
  BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")
  Backtrace:
   1. testthat::expect_warning(...)
   6. ICAMS::VCFsToSBSCatalogs(...)
   7. ICAMS:::InferTransRanges(ref.genome, trans.ranges)
   8. ICAMS:::IsGRCh37(ref.genome)
   9. ICAMS:::NormalizeGenomeArg(x)
  
  ── 3. Error: MutectVCFFilesToCatalog (@test_discarded_variants.R#65)  ──────────
  
  Please install BSgenome.Hsapiens.1000genomes.hs37d5:
  BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")
  Backtrace:
   1. ICAMS::MutectVCFFilesToCatalog(files, ref.genome = "hg19", region = "genome")
   2. ICAMS::VCFsToSBSCatalogs(...)
   3. ICAMS:::InferTransRanges(ref.genome, trans.ranges)
   4. ICAMS:::IsGRCh37(ref.genome)
   5. ICAMS:::NormalizeGenomeArg(x)
  
  ── 4. Error: StrelkaSBSVCFFilesToCatalog (@test_discarded_variants.R#78)  ──────
  
  Please install BSgenome.Hsapiens.1000genomes.hs37d5:
  BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")
  Backtrace:
   1. ICAMS::StrelkaSBSVCFFilesToCatalog(...)
   2. ICAMS::VCFsToSBSCatalogs(...)
   3. ICAMS:::InferTransRanges(ref.genome, trans.ranges)
   4. ICAMS:::IsGRCh37(ref.genome)
   5. ICAMS:::NormalizeGenomeArg(x)
  
  ── 5. Error: StrelkaIDVCFFilesToCatalog (@test_discarded_variants.R#91)  ───────
  
  Please install BSgenome.Hsapiens.1000genomes.hs37d5:
  BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")
  Backtrace:
   1. ICAMS::StrelkaIDVCFFilesToCatalog(...)
   2. ICAMS::VCFsToIDCatalogs(...)
   5. ICAMS::AnnotateIDVCF(...)
   6. ICAMS:::NormalizeGenomeArg(ref.genome)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 158 | SKIPPED: 62 | WARNINGS: 0 | FAILED: 5 ]
  1. Error: Transform a counts catalog with NULL abundance,
            to counts.signature catalog (@test_1TransformCatalog.R#304) 
  2. Error: ReadAndSplitMutectVCFs (@test_discarded_variants.R#15) 
  3. Error: MutectVCFFilesToCatalog (@test_discarded_variants.R#65) 
  4. Error: StrelkaSBSVCFFilesToCatalog (@test_discarded_variants.R#78) 
  5. Error: StrelkaIDVCFFilesToCatalog (@test_discarded_variants.R#91) 
  
  Error: testthat unit tests failed
  Execution halted