Running ‘spelling.R’
  Running ‘test-all.R’ [9s/13s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(nat.nblast)
  Loading required package: rgl
  Loading required package: nat
  Some nat functions depend on a CMTK installation. See ?cmtk and README.md for details.
  
  Attaching package: 'nat'
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, union
  
  > 
  > test_check("nat.nblast")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-smat.r:7:3): calculation of probability matrices is correct ─────
  Error in `NextMethod("[")`: argument "target" is missing, with no default
  Backtrace:
       █
    1. ├─nat.nblast::calc_prob_mat(...) test-smat.r:7:2
    2. └─nat.nblast::calc_dists_dotprods(testneurons[1:3], testneurons[2:5])
    3.   └─plyr::mlply(subset, collect_one_pair, ...)
    4.     └─plyr::alply(...)
    5.       └─plyr::llply(...)
    6.         ├─plyr:::loop_apply(n, do.ply)
    7.         └─(function (i) ...
    8.           └─plyr:::.fun(piece, ...)
    9.             ├─base::do.call(flat, c(args, list(...)))
   10.             └─(function (query, target, ...) ...
   11.               ├─nat.nblast::NeuriteBlast(...)
   12.               │ └─"neuron" %in% class(target)
   13.               ├─target_neurons[target]
   14.               ├─nat:::`[.neuronlist`(target_neurons, target)
   15.               │ └─base::structure(NextMethod("["), class = class(x))
   16.               └─base::NextMethod("[")
  ── Error (test-smat.r:12:3): calculation of score matrices is correct ──────────
  Error in `NextMethod("[")`: argument "target" is missing, with no default
  Backtrace:
       █
    1. ├─nat.nblast::calc_prob_mat(...) test-smat.r:12:2
    2. └─nat.nblast::calc_dists_dotprods(testneurons[1:3], testneurons[2:5])
    3.   └─plyr::mlply(subset, collect_one_pair, ...)
    4.     └─plyr::alply(...)
    5.       └─plyr::llply(...)
    6.         ├─plyr:::loop_apply(n, do.ply)
    7.         └─(function (i) ...
    8.           └─plyr:::.fun(piece, ...)
    9.             ├─base::do.call(flat, c(args, list(...)))
   10.             └─(function (query, target, ...) ...
   11.               ├─nat.nblast::NeuriteBlast(...)
   12.               │ └─"neuron" %in% class(target)
   13.               ├─target_neurons[target]
   14.               ├─nat:::`[.neuronlist`(target_neurons, target)
   15.               │ └─base::structure(NextMethod("["), class = class(x))
   16.               └─base::NextMethod("[")
  ── Error (test-smat.r:30:3): calc_dists_dotprods ───────────────────────────────
  Error in `NextMethod("[")`: argument "target" is missing, with no default
  Backtrace:
       █
    1. ├─testthat::expect_output(...) test-smat.r:30:2
    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(temp, withVisible(code))
    7. │   │     │ └─base::force(code)
    8. │   │     └─base::withVisible(code)
    9. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. └─nat.nblast::calc_dists_dotprods(kcs20[1:5], .progress = "text")
   11.   └─plyr::mlply(subset, collect_one_pair, ...)
   12.     └─plyr::alply(...)
   13.       └─plyr::llply(...)
   14.         ├─plyr:::loop_apply(n, do.ply)
   15.         └─(function (i) ...
   16.           └─plyr:::.fun(piece, ...)
   17.             ├─base::do.call(flat, c(args, list(...)))
   18.             └─(function (query, target, ...) ...
   19.               ├─nat.nblast::NeuriteBlast(...)
   20.               │ └─"neuron" %in% class(target)
   21.               ├─target_neurons[target]
   22.               ├─nat:::`[.neuronlist`(target_neurons, target)
   23.               │ └─base::structure(NextMethod("["), class = class(x))
   24.               └─base::NextMethod("[")
  ── Error (test-smat.r:44:3): create_scoringmatrix wrapper function passes on arguments ──
  Error in `NextMethod("[")`: argument "target" is missing, with no default
  Backtrace:
       █
    1. └─nat.nblast::create_scoringmatrix(...) test-smat.r:44:2
    2.   └─nat.nblast::calc_dists_dotprods(...)
    3.     └─plyr::mlply(subset, collect_one_pair, ...)
    4.       └─plyr::alply(...)
    5.         └─plyr::llply(...)
    6.           ├─plyr:::loop_apply(n, do.ply)
    7.           └─(function (i) ...
    8.             └─plyr:::.fun(piece, ...)
    9.               ├─base::do.call(flat, c(args, list(...)))
   10.               └─(function (query, target, ...) ...
   11.                 ├─nat.nblast::NeuriteBlast(...)
   12.                 │ └─"neuron" %in% class(target)
   13.                 ├─target_neurons[target]
   14.                 ├─nat:::`[.neuronlist`(target_neurons, target)
   15.                 │ └─base::structure(NextMethod("["), class = class(x))
   16.                 └─base::NextMethod("[")
  
  [ FAIL 4 | WARN 4 | SKIP 2 | PASS 42 ]
  Error: Test failures
  Execution halted