Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DGEobj)
  > 
  > test_check("DGEobj")
  Loading required package: stringr
  Loading required package: GenomicRanges
  [ FAIL 9 | WARN 11 | SKIP 0 | PASS 211 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_attributes.R:5:5): attributes.R: showAttributes() ───────────────
  Error in `.requirePackage(package)`: unable to find required package 'S4Vectors'
  Backtrace:
       ▆
    1. ├─testthat::capture_output_lines(showAttributes(t_obj)) at test_attributes.R:5:4
    2. │ └─testthat:::eval_with_output(code, print = print, width = width)
    3. │   ├─withr::with_output_sink(path, withVisible(code))
    4. │   │ └─base::force(code)
    5. │   └─base::withVisible(code)
    6. ├─DGEobj::showAttributes(t_obj)
    7. │ └─base::print(attr(dgeObj[[i]], j))
    8. └─methods:::.extendsForS3(`<chr>`)
    9.   └─methods::extends(Class, maybe = FALSE)
   10.     └─methods::getClassDef(class1)
   11.       └─methods:::.requirePackage(package)
  ── Error (test_reset.R:24:5): reset.R: gene level data ─────────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'GenomicRanges'
  Backtrace:
      ▆
   1. ├─test_t_obj[c(1:10), ] at test_reset.R:24:4
   2. ├─DGEobj:::`[.DGEobj`(test_t_obj, c(1:10), ) at test_reset.R:24:4
   3. │ ├─base::subset(x, row = row)
   4. │ └─DGEobj:::subset.DGEobj(x, row = row)
   5. │   └─base::dim(x[[i]])
   6. └─methods:::.extendsForS3(`<chr>`)
   7.   └─methods::extends(Class, maybe = FALSE)
   8.     └─methods::getClassDef(class1)
   9.       └─methods:::.requirePackage(package)
  ── Failure (test_reset.R:155:5): reset.R: exon level data ──────────────────────
  Names of `test_t_obj` ('counts_orig', 'counts', 'design_orig', 'design', 'exonData_orig', 'exonData') don't match 'counts_orig', 'counts', 'design_orig', 'design', 'exonData_orig', 'exonData', 'granges_orig', 'granges'
  ── Failure (test_reset.R:157:5): reset.R: exon level data ──────────────────────
  Names of `test_t_reset` ('counts_orig', 'counts', 'design_orig', 'design', 'exonData_orig', 'exonData') don't match 'counts_orig', 'counts', 'design_orig', 'design', 'exonData_orig', 'exonData', 'granges_orig', 'granges'
  ── Error (test_reset.R:161:5): reset.R: exon level data ────────────────────────
  Error in `rmItem(test_t_obj, "granges")`: granges does not exist within dgeObj
  Backtrace:
      ▆
   1. └─DGEobj::rmItem(test_t_obj, "granges") at test_reset.R:161:4
  ── Error (test_subset.R:5:5): subset.R: subset() ───────────────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'GenomicRanges'
  Backtrace:
      ▆
   1. ├─base::subset(t_obj, row = c(1:5)) at test_subset.R:5:4
   2. ├─DGEobj:::subset.DGEobj(t_obj, row = c(1:5))
   3. │ └─base::dim(x[[i]])
   4. └─methods:::.extendsForS3(`<chr>`)
   5.   └─methods::extends(Class, maybe = FALSE)
   6.     └─methods::getClassDef(class1)
   7.       └─methods:::.requirePackage(package)
  ── Error (test_subset.R:51:5): subset.R: incorrect usage ───────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'GenomicRanges'
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test_subset.R:51:4
    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. ├─base::subset(t_obj, row = LETTERS)
    7. ├─DGEobj:::subset.DGEobj(t_obj, row = LETTERS)
    8. │ └─base::dim(x[[i]])
    9. └─methods:::.extendsForS3(`<chr>`)
   10.   └─methods::extends(Class, maybe = FALSE)
   11.     └─methods::getClassDef(class1)
   12.       └─methods:::.requirePackage(package)
  ── Error (test_utils.R:16:5): utils.R: inventory() ─────────────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'GenomicRanges'
  Backtrace:
      ▆
   1. ├─DGEobj::inventory(t_obj) at test_utils.R:16:4
   2. │ └─base::dim(dgeObj[[i]])
   3. └─methods:::.extendsForS3(`<chr>`)
   4.   └─methods::extends(Class, maybe = FALSE)
   5.     └─methods::getClassDef(class1)
   6.       └─methods:::.requirePackage(package)
  ── Error (test_utils.R:32:5): utils.R: print() ─────────────────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'GenomicRanges'
  Backtrace:
       ▆
    1. ├─testthat::expect_output(print(t_obj), "ItemName") at test_utils.R:32:4
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat .capture(...)
    4. │   │ └─testthat::capture_output_lines(code, print, width = width)
    5. │   │   └─testthat:::eval_with_output(code, print = print, width = width)
    6. │   │     ├─withr::with_output_sink(path, withVisible(code))
    7. │   │     │ └─base::force(code)
    8. │   │     └─base::withVisible(code)
    9. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. ├─base::print(t_obj)
   11. ├─DGEobj:::print.DGEobj(t_obj)
   12. │ └─DGEobj::inventory(x, verbose = verbose)
   13. │   └─base::dim(dgeObj[[i]])
   14. └─methods:::.extendsForS3(`<chr>`)
   15.   └─methods::extends(Class, maybe = FALSE)
   16.     └─methods::getClassDef(class1)
   17.       └─methods:::.requirePackage(package)
  
  [ FAIL 9 | WARN 11 | SKIP 0 | PASS 211 ]
  Error: Test failures
  In addition: Warning messages:
  1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'GenomicRanges'
  2: In initDGEobj(primaryAssayData = exon_counts, rowData = exon_data,  :
    Unable to build a GRanges object for the gene/exon data.
  Execution halted