Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phyr)
  > 
  > test_check("phyr")
  Dropping tips from the phylogeny that are not in the community data
  1 2 3 4 5 6 7 8 9 10 11 12 13 14 Dropping tips from the phylogeny that are not in the community data
  1  2  3  4  5  6  7  8  9  10  11  12  13  14  Dropping tips from the phylogeny that are not in the community data
  1 2 3 4 5 6 7 8 9 10 11 12 13 14 Dropping tips from the phylogeny that are not in the community data
  1  2  3  4  5  6  7  8  9  10  11  12  13  14  Dropping tips from the phylogeny that are not in the community data
  1 2 3 4 5 6 7 8 9 10 11 12 13 14 Dropping tips from the phylogeny that are not in the community data
  1  2  3  4  5  6  7  8  9  10  11  12  13  14  'as(<matrix>, "dgTMatrix")' is deprecated.
  Use 'as(as(as(., "dMatrix"), "generalMatrix"), "TsparseMatrix")' instead.
  See help("Deprecated") and help("Matrix-deprecated").
  Saving _problems/test-pglmm_compare-15.R
  [ FAIL 1 | WARN 1 | SKIP 3 | PASS 29 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-cor_phylo.R:5:3', 'test-pglmm.R:4:3',
    'test_pglmm_utils.R:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-pglmm_compare.R:15:3'): ignore these tests when on CRAN since they are time consuming ──
  Expected `pglmm_compare(Y ~ X1, family = "binomial", phy = phy, data = sim.dat)` not to throw any errors.
  Actually got a <Rcpp::exception> with message:
    Estimation of B failed. Check for lack of variation in Y. You could try with a smaller s2.init, but this might not help.
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-pglmm_compare.R:15:3
    2. │ └─testthat:::expect_condition_matching_(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─phyr::pglmm_compare(Y ~ X1, family = "binomial", phy = phy, data = sim.dat)
    8.   └─phyr::pglmm(...)
    9.     └─phyr:::communityPGLMM.glmm(...)
   10.       └─phyr:::pglmm_internal_cpp(...)
  
  [ FAIL 1 | WARN 1 | SKIP 3 | PASS 29 ]
  Error:
  ! Test failures.
  Execution halted