Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(nodeSub) # nolint
  Loading required package: Rcpp
  Loading required package: ape
  > 
  > test_check("nodeSub")
  Failed with error:  'object 'crossprod' is not exported by 'namespace:Matrix''
  Failed with error:  'object 'crossprod' is not exported by 'namespace:Matrix''
  Failed with error:  'object 'crossprod' is not exported by 'namespace:Matrix''
  Failed with error:  'object 'crossprod' is not exported by 'namespace:Matrix''
  Failed with error:  'object 'crossprod' is not exported by 'namespace:Matrix''
  Failed with error:  'object 'crossprod' is not exported by 'namespace:Matrix''
  Failed with error:  'object 'crossprod' is not exported by 'namespace:Matrix''
  [ FAIL 21 | WARN 0 | SKIP 2 | PASS 6 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-infer_phylogeny.R:4:3', 'test-sum-stats.R:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-calc_fraction.R:15:5'): calc_fraction use ──────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─nodeSub::calc_required_node_time(phy, s = frac) at test-calc_fraction.R:15:4
    2. │ └─nodeSub::count_hidden(phy)
    3. │   └─nodeSub::reduce_tree(tree)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImportFrom(...)
    6.   │ └─base::asNamespace(ns)
    7.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    8.     ├─base::namespaceImportFrom(...)
    9.     │ └─base::asNamespace(ns)
   10.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11.       └─base::namespaceImportFrom(...)
   12.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-count_hidden.R:19:5'): count_hidden use ────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─nodeSub::reduce_tree(test_tree) at test-count_hidden.R:19:4
    2. └─base::loadNamespace(x)
    3.   ├─base::namespaceImportFrom(...)
    4.   │ └─base::asNamespace(ns)
    5.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    6.     ├─base::namespaceImportFrom(...)
    7.     │ └─base::asNamespace(ns)
    8.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-count_hidden.R:48:5'): count_hidden expectation ────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─base::lapply(test_tree, nodeSub::count_hidden) at test-count_hidden.R:48:4
    2. │ └─nodeSub (local) FUN(X[[i]], ...)
    3. │   └─nodeSub::reduce_tree(tree)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImportFrom(...)
    6.   │ └─base::asNamespace(ns)
    7.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    8.     ├─base::namespaceImportFrom(...)
    9.     │ └─base::asNamespace(ns)
   10.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11.       └─base::namespaceImportFrom(...)
   12.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-create_equal_alignment.R:11:3'): create_equal_alignment ────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─nodeSub::sim_unlinked(...) at test-create_equal_alignment.R:11:2
   2. └─base::loadNamespace(x)
   3.   └─base::namespaceImportFrom(...)
   4.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-create_equal_alignment.R:45:3'): create_equal_alignment_explicit ──
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─nodeSub::sim_unlinked_explicit(...) at test-create_equal_alignment.R:45:2
    2. │ └─nodeSub:::calc_accumulated_substitutions(...)
    3. └─base::loadNamespace(x)
    4.   ├─base::namespaceImportFrom(...)
    5.   │ └─base::asNamespace(ns)
    6.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    7.     ├─base::namespaceImportFrom(...)
    8.     │ └─base::asNamespace(ns)
    9.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   10.       └─base::namespaceImportFrom(...)
   11.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-create_equal_alignment.R:81:3'): create_equal_alignment, nodesub ──
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─nodeSub::sim_normal(x = phy, l = seqlen, rate = sub_rate) at test-create_equal_alignment.R:81:2
   2. └─base::loadNamespace(x)
   3.   └─base::namespaceImportFrom(...)
   4.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-marginal.R:15:3'): marginal ────────────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─nodeSub::sim_normal(x = phy, l = 1000, rate = 0.01) at test-marginal.R:15:2
   2. └─base::loadNamespace(x)
   3.   └─base::namespaceImportFrom(...)
   4.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-relative_node_time.R:18:3'): required_node_time use ────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─nodeSub::calc_required_node_time(focal_tree, s = chosen_fraction) at test-relative_node_time.R:18:2
    2. │ └─nodeSub::count_hidden(phy)
    3. │   └─nodeSub::reduce_tree(tree)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImportFrom(...)
    6.   │ └─base::asNamespace(ns)
    7.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    8.     ├─base::namespaceImportFrom(...)
    9.     │ └─base::asNamespace(ns)
   10.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11.       └─base::namespaceImportFrom(...)
   12.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-relative_node_time.R:77:5'): calc_expected_hidden_nodes, use ───
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─nodeSub::count_hidden(focal_tree) at test-relative_node_time.R:77:4
    2. │ └─nodeSub::reduce_tree(tree)
    3. └─base::loadNamespace(x)
    4.   ├─base::namespaceImportFrom(...)
    5.   │ └─base::asNamespace(ns)
    6.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    7.     ├─base::namespaceImportFrom(...)
    8.     │ └─base::asNamespace(ns)
    9.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   10.       └─base::namespaceImportFrom(...)
   11.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-relative_node_time.R:106:3'): calc_expected_hidden_nodes, abuse ──
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-relative_node_time.R:106:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─nodeSub::calc_expected_hidden_nodes(focal_tree, lambda = 1, mu = 0.3)
    7. └─base::loadNamespace(x)
    8.   ├─base::namespaceImportFrom(...)
    9.   │ └─base::asNamespace(ns)
   10.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11.     ├─base::namespaceImportFrom(...)
   12.     │ └─base::asNamespace(ns)
   13.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   14.       └─base::namespaceImportFrom(...)
   15.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-sim_linked.R:6:3'): sim_linked ─────────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─nodeSub::sim_linked(phy) at test-sim_linked.R:6:2
   2. └─base::loadNamespace(x)
   3.   └─base::namespaceImportFrom(...)
   4.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-sim_linked.R:24:3'): zeros ─────────────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─nodeSub::sim_linked(phy, rate = 0, node_time = 0) at test-sim_linked.R:24:2
   2. └─base::loadNamespace(x)
   3.   └─base::namespaceImportFrom(...)
   4.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-sim_normal.R:6:3'): sim_normal ─────────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-sim_normal.R:6:2
   2.   └─base::namespaceImportFrom(...)
   3.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-sim_normal.R:22:3'): JC ────────────────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-sim_normal.R:22:2
   2.   └─base::namespaceImportFrom(...)
   3.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-sim_normal.R:37:3'): zero ──────────────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-sim_normal.R:37:2
   2.   └─base::namespaceImportFrom(...)
   3.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-sim_normal_explicit.R:6:3'): sim_normal_explicit ───────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─nodeSub::sim_normal(x = phy, l = 10000, rate = 0.01) at test-sim_normal_explicit.R:6:2
   2. └─base::loadNamespace(x)
   3.   └─base::namespaceImportFrom(...)
   4.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-sim_unlinked.R:6:3'): sim_unlinked ─────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─nodeSub::sim_unlinked(phy) at test-sim_unlinked.R:6:2
   2. └─base::loadNamespace(x)
   3.   └─base::namespaceImportFrom(...)
   4.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-sim_unlinked.R:24:3'): zeros ───────────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─nodeSub::sim_unlinked(phy, rate1 = 0, rate2 = 0, node_time = 0) at test-sim_unlinked.R:24:2
   2. └─base::loadNamespace(x)
   3.   └─base::namespaceImportFrom(...)
   4.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-sim_unlinked_explicit.R:6:3'): sim_unlinked_explicit ───────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─nodeSub::sim_unlinked(phy, node_time = 0.1, rate1 = 0.01, rate2 = 0.01) at test-sim_unlinked_explicit.R:6:2
   2. └─base::loadNamespace(x)
   3.   └─base::namespaceImportFrom(...)
   4.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-substitution.R:15:3'): mutations use ───────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-substitution.R:15:2
   2.   └─base::namespaceImportFrom(...)
   3.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-substitution.R:89:3'): matrices ────────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-substitution.R:89:2
   2.   └─base::namespaceImportFrom(...)
   3.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 21 | WARN 0 | SKIP 2 | PASS 6 ]
  Error: Test failures
  Execution halted