Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simphony)
  > 
  > test_check('simphony')
  Saving _problems/test-functional-simphony-9.R
  Saving _problems/test-functional-simphony-33.R
  Saving _problems/test-functional-simphony-47.R
  Saving _problems/test-unit-simphony-32.R
  Saving _problems/test-unit-simphony-59.R
  Saving _problems/test-unit-simphony-72.R
  Saving _problems/test-unit-simphony-83.R
  [ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-functional-simphony.R:7:3'): Abundances are sampled from the correct trend ──
  Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─simphony::simphony(...) at test-functional-simphony.R:7:3
   2.   └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
   3.     ├─...[]
   4.     └─data.table:::`[.data.table`(...)
  ── Error ('test-functional-simphony.R:33:3'): Time-independent statistics from NBD are as expected ──
  Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─simphony::simphony(...) at test-functional-simphony.R:33:3
   2.   └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
   3.     ├─...[]
   4.     └─data.table:::`[.data.table`(...)
  ── Error ('test-functional-simphony.R:46:3'): Time-dependent statistics from NBD are as expected ──
  Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─simphony::simphony(...) at test-functional-simphony.R:46:3
   2.   └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
   3.     ├─...[]
   4.     └─data.table:::`[.data.table`(...)
  ── Error ('test-functional-simphony.R:77:3'): Amplitude and base can be passed as functions ──
  Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(simphony(featureGroups)) at test-functional-simphony.R:77:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─simphony::simphony(featureGroups)
   10.   └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
   11.     ├─...[]
   12.     └─data.table:::`[.data.table`(...)
  ── Error ('test-unit-simphony.R:6:18'): Single condition simulation works ──────
  Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test-unit-simphony.R:6:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:6:18
   10.   └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
   11.     ├─...[]
   12.     └─data.table:::`[.data.table`(...)
  ── Error ('test-unit-simphony.R:15:3'): Multiple condition simulation works ────
  Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(simphony(featureGroupsList)) at test-unit-simphony.R:15:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─simphony::simphony(featureGroupsList)
   10.   └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
   11.     ├─...[]
   12.     └─data.table:::`[.data.table`(...)
  ── Error ('test-unit-simphony.R:30:3'): Number of features and samples simulated are predictable ──
  Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─simphony::simphony(...) at test-unit-simphony.R:30:3
   2.   └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
   3.     ├─...[]
   4.     └─data.table:::`[.data.table`(...)
  ── Error ('test-unit-simphony.R:59:3'): Condition names are as expected ────────
  Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:59:3
   2.   └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
   3.     ├─...[]
   4.     └─data.table:::`[.data.table`(...)
  ── Error ('test-unit-simphony.R:71:3'): Sample names are as expected ───────────
  Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─simphony::simphony(...) at test-unit-simphony.R:71:3
   2.   └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
   3.     ├─...[]
   4.     └─data.table:::`[.data.table`(...)
  ── Error ('test-unit-simphony.R:83:3'): Feature names are as expected ──────────
  Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─simphony::simphony(featureGroups, nFeatures = 20) at test-unit-simphony.R:83:3
   2.   └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
   3.     ├─...[]
   4.     └─data.table:::`[.data.table`(...)
  
  [ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ]
  Error:
  ! Test failures.
  Execution halted