Running ‘test-all.R’ [76s/98s]
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: Classes for Relational Data
  Version 1.13.0 created on 2015-08-31.
  copyright (c) 2005, Carter T. Butts, University of California-Irvine
                      Mark S. Handcock, University of California -- Los Angeles
                      David R. Hunter, Penn State University
                      Martina Morris, University of Washington
                      Skye Bender-deMoll, University of Washington
   For citation information, type citation("network").
   Type help("network-package") to get started.
  
  
  networkDynamic: version 0.9.0, created on 2016-01-12
  Copyright (c) 2016, Carter T. Butts, University of California -- Irvine
                      Ayn Leslie-Cook, University of Washington
                      Pavel N. Krivitsky, University of Wollongong
                      Skye Bender-deMoll, University of Washington
                      with contributions from
                      Zack Almquist, University of California -- Irvine
                      David R. Hunter, Penn State University
                      Li Wang
                      Kirk Li, University of Washington
                      Steven M. Goodreau, University of Washington
                      Jeffrey Horner
                      Martina Morris, University of Washington
  Based on "statnet" project software (statnet.org).
  For license and citation information see statnet.org/attribution
  or type citation("networkDynamic").
  
  Loading required package: tergm
  Loading required package: statnet.common
  
  Attaching package: 'statnet.common'
  
  The following object is masked from 'package:base':
  
      order
  
  Loading required package: ergm
  
  ergm: version 3.8.0, created on 2017-08-18
  Copyright (c) 2017, Mark S. Handcock, University of California -- Los Angeles
                      David R. Hunter, Penn State University
                      Carter T. Butts, University of California -- Irvine
                      Steven M. Goodreau, University of Washington
                      Pavel N. Krivitsky, University of Wollongong
                      Martina Morris, University of Washington
                      with contributions from
                      Li Wang
                      Kirk Li, University of Washington
                      Skye Bender-deMoll, University of Washington
  Based on "statnet" project software (statnet.org).
  For license and citation information see statnet.org/attribution
  or type citation("ergm").
  
  NOTE: Versions before 3.6.1 had a bug in the implementation of the bd()
  constriant which distorted the sampled distribution somewhat. In
  addition, Sampson's Monks datasets had mislabeled vertices. See the
  NEWS and the documentation for more details.
  
  
  tergm: version 3.4.1, created on 2017-09-12
  Copyright (c) 2017, Pavel N. Krivitsky, University of Wollongong
                      Mark S. Handcock, University of California -- Los Angeles
                      with contributions from
                      David R. Hunter, Penn State University
                      Steven M. Goodreau, University of Washington
                      Martina Morris, University of Washington
                      Nicole Bohme Carnegie, New York University
                      Carter T. Butts, University of California -- Irvine
                      Ayn Leslie-Cook, University of Washington
                      Skye Bender-deMoll
                      Li Wang
                      Kirk Li, University of Washington
  Based on "statnet" project software (statnet.org).
  For license and citation information see statnet.org/attribution
  or type citation("tergm").
  
  Returned from SAN Metropolis-Hastings burnin
  SAN Metropolis-Hastings accepted   0.007% of 163840 proposed steps.
  
  * Starting Network Simulation
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 2/25
  Incidence: 2
  Prevalence: 10
  Population: 17
  Births: 0
  Deaths, susceptibles: 6
  Deaths, infecteds: 2
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 3/25
  Incidence: 1
  Prevalence: 8
  Population: 9
  Births: 0
  Deaths, susceptibles: 5
  Deaths, infecteds: 3
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 4/25
  Incidence: 0
  Prevalence: 5
  Population: 5
  Births: 0
  Deaths, susceptibles: 1
  Deaths, infecteds: 3
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 5/25
  Incidence: 0
  Prevalence: 4
  Population: 4
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 1
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 6/25
  Incidence: 0
  Prevalence: 4
  Population: 4
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 7/25
  Incidence: 0
  Prevalence: 3
  Population: 3
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 1
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 8/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 2
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 9/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 10/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 11/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 12/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 13/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 14/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 15/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 16/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 17/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 18/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 19/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 20/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 21/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 22/25
  Incidence: 0
  Prevalence: 1
  Population: 1
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 23/25
  Incidence: 0
  Prevalence: 0
  Population: 0
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 1
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 24/25
  Incidence: 0
  Prevalence: 0
  Population: 0
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 25/25
  Incidence: 0
  Prevalence: 0
  Population: 0
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  * Starting Network Simulation
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 2/25
  Incidence: 0
  Prevalence: 4
  Population: 20
  Births: 1
  Deaths, susceptibles: 0
  Deaths, infecteds: 6
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 3/25
  Incidence: 0
  Prevalence: 2
  Population: 18
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 2
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 4/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 2
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 5/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 6/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 7/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 8/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 9/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 10/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 11/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 12/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 13/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 14/25
  Incidence: 0
  Prevalence: 0
  Population: 16
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 15/25
  Incidence: 0
  Prevalence: 0
  Population: 17
  Births: 1
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 16/25
  Incidence: 0
  Prevalence: 0
  Population: 17
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 17/25
  Incidence: 0
  Prevalence: 0
  Population: 17
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 18/25
  Incidence: 0
  Prevalence: 0
  Population: 18
  Births: 1
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 19/25
  Incidence: 0
  Prevalence: 0
  Population: 19
  Births: 1
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 20/25
  Incidence: 0
  Prevalence: 0
  Population: 19
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 21/25
  Incidence: 0
  Prevalence: 0
  Population: 19
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 22/25
  Incidence: 0
  Prevalence: 0
  Population: 18
  Births: 0
  Deaths, susceptibles: 1
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 23/25
  Incidence: 0
  Prevalence: 0
  Population: 18
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 24/25
  Incidence: 0
  Prevalence: 0
  Population: 17
  Births: 0
  Deaths, susceptibles: 1
  Deaths, infecteds: 0
  ----------------------------
  Epidemic Simulation
  ----------------------------
  Simulation: 1/1
  Timestep: 25/25
  Incidence: 0
  Prevalence: 0
  Population: 17
  Births: 0
  Deaths, susceptibles: 0
  Deaths, infecteds: 0
  ----------------------------
  Network Diagnostics
  -----------------------
  - Simulating 1 networks
  - Calculating formation statistics
  - Calculating duration statistics
  - Calculating dissolution statistics
   EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 1
  Time Steps per Sim: 10
  
  Formation Diagnostics
  ----------------------- 
        Target Sim Mean Pct Diff Sim SD
  edges     15     13.6   -0.093  0.966
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration   20.00    2.000   -0.900  1.414
  Pct Edges Diss   0.05    0.042   -0.152  0.050
  
  Network Diagnostics
  -----------------------
  - Simulating 2 networks
    |**|
  - Calculating formation statistics
  - Calculating duration statistics
    |**|
  - Calculating dissolution statistics
    |**|
   EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 10
  
  Formation Diagnostics
  ----------------------- 
        Target Sim Mean Pct Diff Sim SD
  edges     15    15.75     0.05   1.65
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration   20.00    2.000   -0.900  1.000
  Pct Edges Diss   0.05    0.059    0.182  0.059
  
  Network Diagnostics
  -----------------------
  - Simulating 2 networks
    |**|
  - Calculating formation statistics
  - Calculating duration statistics
    |**|
  - Calculating dissolution statistics
    |**|
   EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 10
  
  Formation Diagnostics
  ----------------------- 
             Target Sim Mean Pct Diff Sim SD
  edges          15    14.95   -0.003  1.638
  concurrent     NA     5.90       NA  0.912
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration   20.00    3.667   -0.817  3.055
  Pct Edges Diss   0.05    0.051    0.013  0.071
  
  Network Diagnostics
  -----------------------
  - Simulating 2 networks
    |**|
  - Calculating formation statistics
  - Calculating duration statistics
    |**|
  - Calculating dissolution statistics
    |**|
   EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 10
  
  Formation Diagnostics
  ----------------------- 
          Target Sim Mean Pct Diff Sim SD
  meandeg     NA     0.83       NA  0.107
  edges       15       NA       NA     NA
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration   20.00    2.500   -0.875  2.121
  Pct Edges Diss   0.05    0.025   -0.494  0.049
  1. Error: Edges only models (@test-netdx.R#53) ---------------------------------
  argument of length 0
  1: plot(dx4, type = "duration") at testthat/test-netdx.R:53
  2: plot.netdx(dx4, type = "duration")
  
  
  Network Diagnostics
  -----------------------
  - Simulating 2 networks
    |**|
  - Calculating formation statistics
  - Calculating duration statistics
    |**|
  - Calculating dissolution statistics
    |**|
   EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 50
  
  Formation Diagnostics
  ----------------------- 
              Target Sim Mean Pct Diff Sim SD
  edges           15    14.07   -0.062  2.471
  mix.loc.0.1     NA     0.00       NA  0.000
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration  40.000   13.250   -0.669 10.428
  Pct Edges Diss  0.025    0.023   -0.089  0.040
  
  Network Diagnostics
  -----------------------
  - Simulating 2 networks
    |**|
  - Calculating formation statistics
  - Calculating duration statistics
    |**|
  - Calculating dissolution statistics
    |**|
   EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 50
  
  Formation Diagnostics
  ----------------------- 
                Target Sim Mean Pct Diff Sim SD
  edges             15    18.49    0.233  3.999
  meandeg           NA     0.74       NA  0.160
  concurrent        NA     8.52       NA  3.295
  nodematch.loc     NA    18.49       NA  3.999
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration  40.000   16.000   -0.600 10.578
  Pct Edges Diss  0.025    0.024   -0.042  0.036
  Returned from SAN Metropolis-Hastings burnin
  SAN Metropolis-Hastings accepted   0.009% of 163840 proposed steps.
  EpiModel Network Diagnostics
  =======================
  Diagnostic Method: Dynamic
  Simulations: 2
  Time Steps per Sim: 50
  
  Formation Diagnostics
  ----------------------- 
              Target Sim Mean Pct Diff Sim SD
  edges           15    12.86   -0.143  4.767
  mix.loc.0.1      0     0.00      NaN  0.000
  
  Dissolution Diagnostics
  ----------------------- 
                 Target Sim Mean Pct Diff Sim SD
  Edge Duration  40.000   14.273   -0.643 12.386
  Pct Edges Diss  0.025    0.023   -0.080  0.043
  Returned from SAN Metropolis-Hastings burnin
  SAN Metropolis-Hastings accepted   0.031% of 163840 proposed steps.
  Returned from SAN Metropolis-Hastings burnin
  SAN Metropolis-Hastings accepted   0.002% of 163840 proposed steps.
  Sampler accepted  70.296% of 1048576 proposed steps.
  Sampler accepted  68.449% of 4194304 proposed steps.
  
  Network Diagnostics
  -----------------------
  - Simulating 250 networks
  - Calculating formation statistics
  * 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	testthat results ================================================================
  OK: 278 SKIPPED: 76 FAILED: 1
  1. Error: Edges only models (@test-netdx.R#53) 
  
  Error: testthat unit tests failed
  Execution halted