Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hillR)
  > 
  > test_check("hillR")
  [ FAIL 6 | WARN 0 | SKIP 9 | PASS 31 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • vegetarian cannot be loaded (9): 'test_hill_taxa.R:6:3',
    'test_hill_taxa.R:15:3', 'test_hill_taxa.R:24:3', 'test_hill_taxa.R:33:3',
    'test_hill_taxa.R:42:3', 'test_hill_taxa.R:57:3', 'test_hill_taxa.R:72:3',
    'test_hill_taxa.R:87:3', 'test_hill_taxa.R:102:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_hill_phyl.R:7:3'): PD of each site ─────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─hillR::hill_phylo(comm = dummy$abun, tree, q = 0) at test_hill_phyl.R:7:2
    2. │ └─hillR:::dat_prep_phylo(comm, tree)
    3. │   └─base::lapply(...)
    4. │     └─hillR (local) FUN(X[[i]], ...)
    5. └─base::loadNamespace(x)
    6.   ├─base::namespaceImportFrom(...)
    7.   │ └─base::asNamespace(ns)
    8.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    9.     ├─base::namespaceImportFrom(...)
   10.     │ └─base::asNamespace(ns)
   11.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   12.       └─base::namespaceImportFrom(...)
   13.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_hill_phyl.R:11:3'): phylogenetic similarity should be between 0 and 1; q = 0 ──
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─hillR::hill_phylo_parti(comm = dummy$abun, tree, q = 0) at test_hill_phyl.R:11:2
    2. │ └─hillR:::dat_prep_phylo(comm, tree)
    3. │   └─base::lapply(...)
    4. │     └─hillR (local) FUN(X[[i]], ...)
    5. └─base::loadNamespace(x)
    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::asNamespace(ns)
   11.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   12.       └─base::namespaceImportFrom(...)
   13.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_hill_phyl.R:19:3'): phylogenetic similarity should be between 0 and 1; q = 1 ──
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─hillR::hill_phylo_parti(comm = dummy$abun, tree, q = 1) at test_hill_phyl.R:19:2
    2. │ └─hillR:::dat_prep_phylo(comm, tree)
    3. │   └─base::lapply(...)
    4. │     └─hillR (local) FUN(X[[i]], ...)
    5. └─base::loadNamespace(x)
    6.   ├─base::namespaceImportFrom(...)
    7.   │ └─base::asNamespace(ns)
    8.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    9.     ├─base::namespaceImportFrom(...)
   10.     │ └─base::asNamespace(ns)
   11.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   12.       └─base::namespaceImportFrom(...)
   13.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_hill_phyl.R:27:3'): phylogenetic similarity should be between 0 and 1; q = 2 ──
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─hillR::hill_phylo_parti(comm = dummy$abun, tree, q = 2) at test_hill_phyl.R:27:2
    2. │ └─hillR:::dat_prep_phylo(comm, tree)
    3. │   └─base::lapply(...)
    4. │     └─hillR (local) FUN(X[[i]], ...)
    5. └─base::loadNamespace(x)
    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::asNamespace(ns)
   11.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   12.       └─base::namespaceImportFrom(...)
   13.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_hill_phyl.R:35:3'): pairwise similarity ────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─hillR::hill_phylo_parti_pairwise(...) at test_hill_phyl.R:35:2
    2. │ └─hillR::hill_phylo_parti(...)
    3. │   └─hillR:::dat_prep_phylo(comm, tree)
    4. │     └─base::lapply(...)
    5. │       └─hillR (local) FUN(X[[i]], ...)
    6. └─base::loadNamespace(x)
    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::asNamespace(ns)
   12.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   13.       └─base::namespaceImportFrom(...)
   14.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_hill_phyl.R:55:3'): when N = 2, hill_phylo_parti equals Sorensen ──
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─hillR::hill_phylo_parti(toy.comm, toy.tree) at test_hill_phyl.R:55:2
    2. │ └─hillR:::dat_prep_phylo(comm, tree)
    3. │   └─base::lapply(...)
    4. │     └─hillR (local) FUN(X[[i]], ...)
    5. └─base::loadNamespace(x)
    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::asNamespace(ns)
   11.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   12.       └─base::namespaceImportFrom(...)
   13.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 6 | WARN 0 | SKIP 9 | PASS 31 ]
  Error: Test failures
  Execution halted