Package: compositional.mle
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘case-studies.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘case-studies.Rmd’
  
  --- re-building ‘getting-started.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘getting-started.Rmd’
  
  --- re-building ‘mle-ecosystem.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘mle-ecosystem.Rmd’
  
  --- re-building ‘strategy-design.Rmd’ using rmarkdown
  
  Quitting from strategy-design.Rmd:184-201 [diagnose]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `xy.coords()`:
  ! 'x' is a list, but does not have components 'x' and 'y'
  ---
  Backtrace:
      ▆
   1. ├─base::plot(result_traced, which = c("loglike", "path"))
   2. └─graphics::plot.default(result_traced, which = c("loglike", "path"))
   3.   └─grDevices::xy.coords(x, y, xlabel, ylabel, log)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'strategy-design.Rmd' failed with diagnostics:
  'x' is a list, but does not have components 'x' and 'y'
  --- failed re-building ‘strategy-design.Rmd’
  
  --- re-building ‘theory-and-intuition.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘theory-and-intuition.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘strategy-design.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: compositional.mle
Check: tests
New result: ERROR
    Running ‘testthat.R’ [6s/7s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(compositional.mle)
    Loading required package: algebraic.mle
    
    Attaching package: 'algebraic.mle'
    
    The following object is masked from 'package:testthat':
    
        expectation
    
    > 
    > test_check("compositional.mle")
    Saving _problems/test-algebraic-mle-generics-12.R
    Saving _problems/test-algebraic-mle-generics-35.R
    Saving _problems/test-algebraic-mle-generics-46.R
    Saving _problems/test-algebraic-mle-generics-58.R
    Saving _problems/test-algebraic-mle-generics-70.R
    Saving _problems/test-algebraic-mle-generics-84.R
    Saving _problems/test-annealing-50.R
    Saving _problems/test-coordinate-53.R
    Saving _problems/test-generic-functions-14.R
    Saving _problems/test-generic-functions-15.R
    Saving _problems/test-generic-functions-50.R
    Saving _problems/test-generic-functions-105.R
    Saving _problems/test-gradient-ascent-13.R
    Saving _problems/test-integration-45.R
    Saving _problems/test-integration-57.R
    Saving _problems/test-integration-92.R
    Saving _problems/test-integration-105.R
    Saving _problems/test-integration-118.R
    Saving _problems/test-integration-136.R
    Saving _problems/test-integration-147.R
    Saving _problems/test-meta-solvers-104.R
    Saving _problems/test-meta-solvers-128.R
    Saving _problems/test-meta-solvers-158.R
    Saving _problems/test-meta-solvers-174.R
    Saving _problems/test-meta-solvers-192.R
    Saving _problems/test-meta-solvers-204.R
    Saving _problems/test-meta-solvers-228.R
    Saving _problems/test-meta-solvers-247.R
    Saving _problems/test-newton-raphson-14.R
    Saving _problems/test-plot-34.R
    Saving _problems/test-plot-48.R
    Saving _problems/test-plot-78.R
    Saving _problems/test-solvers-9.R
    Saving _problems/test-solvers-20.R
    Saving _problems/test-solvers-32.R
    Saving _problems/test-solvers-43.R
    Saving _problems/test-solvers-54.R
    Saving _problems/test-solvers-67.R
    [ FAIL 39 | WARN 0 | SKIP 0 | PASS 265 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-algebraic-mle-generics.R:12:3'): algebraic.mle generics work on gradient_ascent result ──
    Error in `loglik_val(result)`: could not find function "loglik_val"
    Backtrace:
        ▆
     1. └─testthat::expect_true(is.numeric(loglik_val(result))) at test-algebraic-mle-generics.R:12:3
     2.   └─testthat::quasi_label(enquo(object), label)
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Error ('test-algebraic-mle-generics.R:35:3'): algebraic.mle generics work on newton_raphson result ──
    Error in `loglik_val(result)`: could not find function "loglik_val"
    Backtrace:
        ▆
     1. └─testthat::expect_true(is.numeric(loglik_val(result))) at test-algebraic-mle-generics.R:35:3
     2.   └─testthat::quasi_label(enquo(object), label)
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Error ('test-algebraic-mle-generics.R:46:3'): algebraic.mle generics work on bfgs result ──
    Error in `loglik_val(result)`: could not find function "loglik_val"
    Backtrace:
        ▆
     1. └─testthat::expect_true(is.numeric(loglik_val(result))) at test-algebraic-mle-generics.R:46:3
     2.   └─testthat::quasi_label(enquo(object), label)
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Error ('test-algebraic-mle-generics.R:58:3'): algebraic.mle generics work on composed chain result ──
    Error in `loglik_val(result)`: could not find function "loglik_val"
    Backtrace:
        ▆
     1. └─testthat::expect_true(is.numeric(loglik_val(result))) at test-algebraic-mle-generics.R:58:3
     2.   └─testthat::quasi_label(enquo(object), label)
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Error ('test-algebraic-mle-generics.R:70:3'): algebraic.mle generics work on race result ──
    Error in `loglik_val(result)`: could not find function "loglik_val"
    Backtrace:
        ▆
     1. └─testthat::expect_true(is.numeric(loglik_val(result))) at test-algebraic-mle-generics.R:70:3
     2.   └─testthat::quasi_label(enquo(object), label)
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Error ('test-algebraic-mle-generics.R:84:3'): algebraic.mle generics work on with_restarts result ──
    Error in `loglik_val(result)`: could not find function "loglik_val"
    Backtrace:
        ▆
     1. └─testthat::expect_true(is.numeric(loglik_val(result))) at test-algebraic-mle-generics.R:84:3
     2.   └─testthat::quasi_label(enquo(object), label)
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Failure ('test-annealing.R:50:3'): sim_anneal returns proper result structure ──
    Expected `result` to inherit from "mle_numerical".
    Actual class: "mle_sim_anneal"/"mle_fit_numerical"/"mle_fit".
    ── Failure ('test-coordinate.R:53:3'): coordinate_ascent returns proper result structure ──
    Expected `result` to inherit from "mle_numerical".
    Actual class: "mle_coordinate_ascent"/"mle_fit_numerical"/"mle_fit".
    ── Failure ('test-generic-functions.R:14:3'): mle_numerical objects from algebraic.mle work correctly ──
    Expected `inherits(result, "mle_numerical")` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-generic-functions.R:15:3'): mle_numerical objects from algebraic.mle work correctly ──
    Expected `inherits(result, "mle")` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-generic-functions.R:50:3'): is_mle_numerical works correctly ──
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-generic-functions.R:105:3'): generic functions work with solver results ──
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-gradient-ascent.R:13:3'): gradient_ascent works on simple quadratic problem ──
    Expected `result` to inherit from "mle_numerical".
    Actual class: "mle_gradient_ascent"/"mle_fit_numerical"/"mle_fit".
    ── Failure ('test-integration.R:45:3'): Sequential composition works ───────────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-integration.R:57:3'): with_restarts improves robustness ──────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-integration.R:92:3'): BFGS solver works on simple problem ────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-integration.R:105:3'): Nelder-Mead solver works ──────────────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-integration.R:118:3'): L-BFGS-B respects bounds ──────────────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-integration.R:136:3'): unless_converged applies refinement when needed ──
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-integration.R:147:3'): Parallel race selects best result ─────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-meta-solvers.R:104:3'): with_restarts basic functionality ────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-meta-solvers.R:128:3'): with_restarts respects problem constraints ──
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-meta-solvers.R:158:3'): sequential composition %>>% works ────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-meta-solvers.R:174:3'): three-stage composition works ────────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-meta-solvers.R:192:3'): unless_converged only runs refinement on failure ──
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-meta-solvers.R:204:3'): parallel race %|% works ──────────────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-meta-solvers.R:228:3'): race() with parallel = TRUE works ────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-meta-solvers.R:247:3'): race() without parallel works ────────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-newton-raphson.R:14:3'): newton_raphson works on simple quadratic problem ──
    Expected `result` to inherit from "mle_numerical".
    Actual class: "mle_newton_raphson"/"mle_fit_numerical"/"mle_fit".
    ── Error ('test-plot.R:15:5'): plot.mle_numerical works with trace data ────────
    Error in `xy.coords(x, y, xlabel, ylabel, log)`: 'x' is a list, but does not have components 'x' and 'y'
    Backtrace:
         ▆
      1. ├─testthat::expect_silent(...) at test-plot.R:12:3
      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. ├─base::plot(result) at test-plot.R:15:5
     10. └─graphics::plot.default(result)
     11.   └─grDevices::xy.coords(x, y, xlabel, ylabel, log)
    ── Error ('test-plot.R:34:3'): plot.mle_numerical warns when no trace data ─────
    Error in `xy.coords(x, y, xlabel, ylabel, log)`: 'x' is a list, but does not have components 'x' and 'y'
    Backtrace:
        ▆
     1. ├─testthat::expect_warning(plot(result), "No trace data") at test-plot.R:34:3
     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. ├─base::plot(result)
     8. └─graphics::plot.default(result)
     9.   └─grDevices::xy.coords(x, y, xlabel, ylabel, log)
    ── Error ('test-plot.R:48:3'): optimization_path extracts trace as data frame ──
    Error in `UseMethod("optimization_path")`: no applicable method for 'optimization_path' applied to an object of class "c('mle_gradient_ascent', 'mle_fit_numerical', 'mle_fit')"
    Backtrace:
        ▆
     1. └─compositional.mle::optimization_path(result) at test-plot.R:48:3
    ── Error ('test-plot.R:78:3'): optimization_path warns when no trace data ──────
    Error in `UseMethod("optimization_path")`: no applicable method for 'optimization_path' applied to an object of class "c('mle_gradient_ascent', 'mle_fit_numerical', 'mle_fit')"
    Backtrace:
        ▆
     1. ├─testthat::expect_warning(path <- optimization_path(result), "No trace data") at test-plot.R:78:3
     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. └─compositional.mle::optimization_path(result)
    ── Failure ('test-solvers.R:9:3'): gradient_ascent solves normal MLE ───────────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-solvers.R:20:3'): newton_raphson solves normal MLE ───────────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-solvers.R:32:3'): bfgs solves normal MLE ─────────────────────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-solvers.R:43:3'): nelder_mead solves normal MLE ──────────────
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-solvers.R:54:3'): grid_search finds reasonable starting point ──
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── Failure ('test-solvers.R:67:3'): random_search finds reasonable starting point ──
    Expected `is_mle_numerical(result)` to be TRUE.
    Differences:
    `actual`:   FALSE
    `expected`: TRUE 
    
    
    [ FAIL 39 | WARN 0 | SKIP 0 | PASS 265 ]
    Error:
    ! Test failures.
    Execution halted

Package: likelihood.model
Check: whether package can be installed
New result: ERROR
  Installation failed.

Package: maskedcauses
Check: package dependencies
New result: ERROR
  Package required but not available: ‘likelihood.model’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.