Running ‘testthat.R’ [8s/13s]
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
  Loading required package: stats4
  Loading required package: BiocGenerics
  
  Attaching package: 'BiocGenerics'
  
  The following objects are masked from 'package:stats':
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from 'package:base':
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which.max, which.min
  
  Loading required package: S4Vectors
  
  Attaching package: 'S4Vectors'
  
  The following objects are masked from 'package:base':
  
      I, expand.grid, unname
  
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 223 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_reset.R:24:5): reset.R: gene level data ─────────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'edgeR'
  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.     └─x[[i]][row, col]
    6.       └─methods `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
    7.         └─methods:::.findInheritedMethods(classes, fdef, mtable)
    8.           └─methods::getClass(cl1, where = where, .Force = TRUE)
    9.             └─methods::getClassDef(Class, where)
   10.               └─methods:::.requirePackage(package)
  ── Error (test_subset.R:5:5): subset.R: subset() ───────────────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'edgeR'
  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.   └─x[[i]][row, col]
   4.     └─methods `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
   5.       └─methods:::.findInheritedMethods(classes, fdef, mtable)
   6.         └─methods::getClass(cl1, where = where, .Force = TRUE)
   7.           └─methods::getClassDef(Class, where)
   8.             └─methods:::.requirePackage(package)
  ── Error (test_subset.R:51:5): subset.R: incorrect usage ───────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'edgeR'
  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.   └─x[[i]][row, col]
    9.     └─methods `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
   10.       └─methods:::.findInheritedMethods(classes, fdef, mtable)
   11.         └─methods::getClass(cl1, where = where, .Force = TRUE)
   12.           └─methods::getClassDef(Class, where)
   13.             └─methods:::.requirePackage(package)
  ── Error (test_utils.R:16:5): utils.R: inventory() ─────────────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'edgeR'
  Backtrace:
      ▆
   1. └─DGEobj::inventory(t_obj) at test_utils.R:16:4
   2.   └─methods dim(dgeObj[[i]])
   3.     └─methods `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
   4.       └─methods:::.findInheritedMethods(classes, fdef, mtable)
   5.         └─methods::getClass(cl1, where = where, .Force = TRUE)
   6.           └─methods::getClassDef(Class, where)
   7.             └─methods:::.requirePackage(package)
  ── Error (test_utils.R:32:5): utils.R: print() ─────────────────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'edgeR'
  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.     └─methods dim(dgeObj[[i]])
   14.       └─methods `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
   15.         └─methods:::.findInheritedMethods(classes, fdef, mtable)
   16.           └─methods::getClass(cl1, where = where, .Force = TRUE)
   17.             └─methods::getClassDef(Class, where)
   18.               └─methods:::.requirePackage(package)
  
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 223 ]
  Error: Test failures
  Execution halted