Running ‘test-all.R’ [100s/147s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("EpiModel")
  Loading required package: EpiModel
  Loading required package: deSolve
  Loading required package: networkDynamic
  Loading required package: network
  
  'network' 1.17.1 (2021-06-12), part of the Statnet Project
  * 'news(package="network")' for changes since last version
  * 'citation("network")' for citation information
  * 'https://statnet.org' for help, support, and other information
  
  
  'networkDynamic' 0.11.0 (2021-06-12), part of the Statnet Project
  * 'news(package="networkDynamic")' for changes since last version
  * 'citation("networkDynamic")' for citation information
  * 'https://statnet.org' for help, support, and other information
  
  Loading required package: tergm
  Loading required package: ergm
  
  'ergm' 4.0.1 (2021-06-20), part of the Statnet Project
  * 'news(package="ergm")' for changes since last version
  * 'citation("ergm")' for citation information
  * 'https://statnet.org' for help, support, and other information
  
  'ergm' 4 is a major update that introduces some backwards-incompatible
  changes. Please type 'news(package="ergm")' for a list of major
  changes.
  
  
  'tergm' 4.0.1 (2021-06-24), part of the Statnet Project
  * 'news(package="tergm")' for changes since last version
  * 'citation("tergm")' for citation information
  * 'https://statnet.org' for help, support, and other information
  
  
  Attaching package: 'tergm'
  
  The following object is masked from 'package:ergm':
  
      snctrl
  
  Loading required package: tergmLite
  EpiModel NOTE: EpiModel 2.0 implements significant changes to the
  EpiModel application programming interface (API), which may require
  updates to model code written under EpiModel 1.x. See
  https://epimodel.org/ for migration guidance.
  
  
  Starting Network Simulation...
  Sim = 1/5
  Sim = 2/5
  Sim = 3/5
  Sim = 4/5
  Sim = 5/5
  Starting Network Simulation...
  Sim = 1/5
  Sim = 2/5
  Sim = 3/5
  Sim = 4/5
  Sim = 5/5
  Starting Network Simulation...
  Starting Network Simulation...
  Starting Network Simulation...
  Starting Network Simulation...
  Starting Network Simulation...
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 2/5
  Prevalence: 11
  Population Size: 1000
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 3/5
  Prevalence: 14
  Population Size: 1000
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 4/5
  Prevalence: 19
  Population Size: 1000
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 5/5
  Prevalence: 23
  Population Size: 1000
  ----------------------------
  Starting Network Simulation...EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 1
  Time Steps per Sim: 10
  
  Formation Diagnostics
  ----------------------- 
        Target Sim Mean Pct Diff Sim SD
  edges     15     11.1      -26     NA
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration   20.00   19.551   -2.247     NA
  Pct Edges Diss   0.05    0.095   90.660     NA
  EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 10
  
  Formation Diagnostics
  ----------------------- 
        Target Sim Mean Pct Diff Sim SD
  edges     15       16    6.667   1.98
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration   20.00   19.861   -0.693  0.285
  Pct Edges Diss   0.05    0.053    5.344  0.001
  EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 10
  
  Formation Diagnostics
  ----------------------- 
             Target Sim Mean Pct Diff Sim SD
  edges          15    14.40       -4  4.243
  concurrent     NA     5.15       NA  3.465
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration   20.00   20.112    0.560  0.641
  Pct Edges Diss   0.05    0.047   -5.035  0.018
  EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 10
  
  Formation Diagnostics
  ----------------------- 
          Target Sim Mean Pct Diff Sim SD
  meandeg     NA    0.616       NA   0.17
  edges       15       NA       NA     NA
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration   20.00   19.739   -1.303  0.009
  Pct Edges Diss   0.05    0.050    0.791  0.013
  
  Network Diagnostics
  -----------------------
  - Simulating 2 networks
    |**|
  - Calculating formation statistics
  - Calculating duration statistics
    |**|
  - Calculating dissolution statistics
    |**|
   
  Network Diagnostics
  -----------------------
  - Simulating 1 network
  - Calculating formation statisticsEpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 50
  
  Formation Diagnostics
  ----------------------- 
                      Target Sim Mean Pct Diff Sim SD
  edges                   15    15.07    0.467   2.22
  offset(mix.loc.0.1)     NA     0.00       NA   0.00
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration  40.000   40.786    1.964  0.919
  Pct Edges Diss  0.025    0.023   -8.260  0.006
  EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 50
  
  Formation Diagnostics
  ----------------------- 
                Target Sim Mean Pct Diff Sim SD
  edges             15   16.350        9  1.711
  meandeg           NA    0.654       NA  0.068
  concurrent        NA    6.700       NA  1.245
  nodematch.loc     NA   16.350       NA  1.711
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration  40.000   39.845   -0.387  0.047
  Pct Edges Diss  0.025    0.025   -1.416  0.000
  EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 50
  
  Formation Diagnostics
  ----------------------- 
              Target Sim Mean Pct Diff Sim SD
  edges           15    14.67     -2.2  1.966
  mix.loc.0.1      0     0.00      NaN  0.000
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration  40.000   38.907   -2.733  0.927
  Pct Edges Diss  0.025    0.021  -14.531  0.003
  
  Network Diagnostics
  -----------------------
  - Simulating 250 networks
  - Calculating formation statistics
  Network Diagnostics
  -----------------------
  - Simulating 2 networks
    |
  Network Diagnostics
  -----------------------
  - Simulating 2 networks
    |**|
  - Calculating formation statistics
  - Calculating duration statistics
    |**|
  - Calculating dissolution statistics
    |**|
   
  Network Diagnostics
  -----------------------
  - Simulating 2 networks
    |
  Network Diagnostics
  -----------------------
  - Simulating 2 networks
    |**|
  - Calculating formation statistics
  - Calculating duration statistics
    |**|
  - Calculating dissolution statistics
    |**|
   
  Starting Network Simulation...
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 2/5
  Prevalence: 12
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 3/5
  Prevalence: 13
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 4/5
  Prevalence: 13
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 5/5
  Prevalence: 13
  Population Size: 50
  ----------------------------
  Starting Network Simulation...
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 2/10
  Prevalence: 13
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 3/10
  Prevalence: 15
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 4/10
  Prevalence: 16
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 5/10
  Prevalence: 18
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 6/10
  Prevalence: 19
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 7/10
  Prevalence: 19
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 8/10
  Prevalence: 19
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 9/10
  Prevalence: 20
  Population Size: 50
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 10/10
  Prevalence: 21
  Population Size: 50
  ----------------------------
  Starting Network Simulation...
  Sim = 1/1
  1/10	
  2/10	
  3/10	
  4/10	
  5/10	
  6/10	
  7/10	
  8/10	
  9/10	
  10/10	══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (82)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-net-tergmLite.R:20:3): tergmLite: 1G, Closed ────────────────────
  Error: The combination of class (f), model constraints and hints ('.attributes' and 'sparse'), reference measure ("Bernoulli"), proposal weighting (default), and conjunctions and disjunctions is not implemented. Check your arguments for typos. 
  Backtrace:
       █
    1. └─EpiModel::netsim(est, param, init, control) test-net-tergmLite.R:20:2
    2.   └─base::lapply(...)
    3.     └─EpiModel:::FUN(X[[i]], ...)
    4.       └─EpiModel:::netsim_loop(x, param, init, control, s)
    5.         ├─base::withCallingHandlers(...)
    6.         ├─base::do.call(...)
    7.         └─(function (x, param, init, control, s) ...
    8.           └─tergmLite::init_tergmLite(dat)
    9.             └─tergmLite:::stergm_prep(...)
   10.               ├─ergm::ergm_proposal(...)
   11.               └─ergm:::ergm_proposal.formula(...)
   12.                 ├─ergm::ergm_proposal(conlist, arguments, nw, ..., term.options = term.options)
   13.                 └─ergm:::ergm_proposal.ergm_conlist(...)
   14.                   └─ergm:::select_ergm_proposal(...)
  ── Error (test-net-tergmLite.R:65:3): tergmLite: 2G, Closed ────────────────────
  Error: The combination of class (f), model constraints and hints ('.attributes' and 'sparse'), reference measure ("Bernoulli"), proposal weighting (default), and conjunctions and disjunctions is not implemented. Check your arguments for typos. 
  Backtrace:
       █
    1. └─EpiModel::netsim(est, param, init, control) test-net-tergmLite.R:65:2
    2.   └─base::lapply(...)
    3.     └─EpiModel:::FUN(X[[i]], ...)
    4.       └─EpiModel:::netsim_loop(x, param, init, control, s)
    5.         ├─base::withCallingHandlers(...)
    6.         ├─base::do.call(...)
    7.         └─(function (x, param, init, control, s) ...
    8.           └─tergmLite::init_tergmLite(dat)
    9.             └─tergmLite:::stergm_prep(...)
   10.               ├─ergm::ergm_proposal(...)
   11.               └─ergm:::ergm_proposal.formula(...)
   12.                 ├─ergm::ergm_proposal(conlist, arguments, nw, ..., term.options = term.options)
   13.                 └─ergm:::ergm_proposal.ergm_conlist(...)
   14.                   └─ergm:::select_ergm_proposal(...)
  ── Error (test-net-tergmLite.R:113:3): tergmLite: 1G, Open ─────────────────────
  Error: The combination of class (f), model constraints and hints ('.attributes' and 'sparse'), reference measure ("Bernoulli"), proposal weighting (default), and conjunctions and disjunctions is not implemented. Check your arguments for typos. 
  Backtrace:
       █
    1. └─EpiModel::netsim(est, param, init, control) test-net-tergmLite.R:113:2
    2.   └─base::lapply(...)
    3.     └─EpiModel:::FUN(X[[i]], ...)
    4.       └─EpiModel:::netsim_loop(x, param, init, control, s)
    5.         ├─base::withCallingHandlers(...)
    6.         ├─base::do.call(...)
    7.         └─(function (x, param, init, control, s) ...
    8.           └─tergmLite::init_tergmLite(dat)
    9.             └─tergmLite:::stergm_prep(...)
   10.               ├─ergm::ergm_proposal(...)
   11.               └─ergm:::ergm_proposal.formula(...)
   12.                 ├─ergm::ergm_proposal(conlist, arguments, nw, ..., term.options = term.options)
   13.                 └─ergm:::ergm_proposal.ergm_conlist(...)
   14.                   └─ergm:::select_ergm_proposal(...)
  ── Error (test-net-tergmLite.R:167:3): tergmLite: 2G, Open ─────────────────────
  Error: The combination of class (f), model constraints and hints ('.attributes' and 'sparse'), reference measure ("Bernoulli"), proposal weighting (default), and conjunctions and disjunctions is not implemented. Check your arguments for typos. 
  Backtrace:
       █
    1. └─EpiModel::netsim(est, param, init, control) test-net-tergmLite.R:167:2
    2.   └─base::lapply(...)
    3.     └─EpiModel:::FUN(X[[i]], ...)
    4.       └─EpiModel:::netsim_loop(x, param, init, control, s)
    5.         ├─base::withCallingHandlers(...)
    6.         ├─base::do.call(...)
    7.         └─(function (x, param, init, control, s) ...
    8.           └─tergmLite::init_tergmLite(dat)
    9.             └─tergmLite:::stergm_prep(...)
   10.               ├─ergm::ergm_proposal(...)
   11.               └─ergm:::ergm_proposal.formula(...)
   12.                 ├─ergm::ergm_proposal(conlist, arguments, nw, ..., term.options = term.options)
   13.                 └─ergm:::ergm_proposal.ergm_conlist(...)
   14.                   └─ergm:::select_ergm_proposal(...)
  ── Error (test-net-tergmLite.R:221:3): Models with duration = 1 ────────────────
  Error: argument "state" is missing, with no default
  Backtrace:
       █
    1. └─EpiModel::netsim(est, param, init, control) test-net-tergmLite.R:221:2
    2.   └─base::lapply(...)
    3.     └─EpiModel:::FUN(X[[i]], ...)
    4.       └─EpiModel:::netsim_loop(x, param, init, control, s)
    5.         ├─base::withCallingHandlers(...)
    6.         ├─base::do.call(control[[current_mod]], list(dat, at))
    7.         └─(function (dat, at) ...
    8.           └─tergmLite::simulate_ergm(p = dat$p[[1]], el = dat$el[[1]], coef = nwparam$coef.form)
    9.             └─tergmLite:::ergm_getMCMCsample(...)
   10.               └─ergm::ergm_MCMC_slave(...)
   11.                 └─ergm::is.valued(state)
  ── Error (test-newmodules.R:118:3): New network models vignette example ────────
  Error: The combination of class (f), model constraints and hints ('.attributes' and 'sparse'), reference measure ("Bernoulli"), proposal weighting (default), and conjunctions and disjunctions is not implemented. Check your arguments for typos. 
  Backtrace:
       █
    1. └─EpiModel::netsim(est, param, init, control) test-newmodules.R:118:2
    2.   └─base::lapply(...)
    3.     └─EpiModel:::FUN(X[[i]], ...)
    4.       └─EpiModel:::netsim_loop(x, param, init, control, s)
    5.         ├─base::withCallingHandlers(...)
    6.         ├─base::do.call(...)
    7.         └─(function (x, param, init, control, s) ...
    8.           └─tergmLite::init_tergmLite(dat)
    9.             └─tergmLite:::stergm_prep(...)
   10.               ├─ergm::ergm_proposal(...)
   11.               └─ergm:::ergm_proposal.formula(...)
   12.                 ├─ergm::ergm_proposal(conlist, arguments, nw, ..., term.options = term.options)
   13.                 └─ergm:::ergm_proposal.ergm_conlist(...)
   14.                   └─ergm:::select_ergm_proposal(...)
  
  [ FAIL 6 | WARN 3 | SKIP 82 | PASS 379 ]
  Error: Test failures
  Execution halted