• using R version 4.5.2 (2025-10-31)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-10) 14.3.0     GNU Fortran (Debian 14.3.0-10) 14.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘epiworldR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘epiworldR’ version ‘0.10.0.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘epiworldR’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/0s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/0s] OK
• checking whether startup messages can be suppressed ... [0s/1s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [9s/12s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [9s/12s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [33s/45s] ERROR   Running ‘tinytest.R’ [33s/44s] Running the tests in ‘tests/tinytest.R’ failed. Complete output:   >   > if (requireNamespace("tinytest", quietly = TRUE)) {   +   + test_tmat_matches_expected <- function(tmat) {   + # Check for out of bounds values   + tinytest::expect_false(any(tmat < 0))   + tinytest::expect_false(any(tmat > 1))   + }   +   + tinytest::test_package("epiworldR")   + }   Thank you for using epiworldR! Please consider citing it in your work.   You can find the citation information by running     citation("epiworldR")      test-agents-and-dist-virus-tool.R 0 tests   test-agents-and-dist-virus-tool.R 0 tests _________________________________________________________________________   Running the model...   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-agents-and-dist-virus-tool.R 0 tests   test-agents-and-dist-virus-tool.R 0 tests   test-agents-and-dist-virus-tool.R 1 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 1 tests [0;32mOK [0m Starting multiple runs (100) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-agents-and-dist-virus-tool.R 1 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 1 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 1 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 1 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 2 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 2 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 2 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 2 tests [0;32mOK [0m _________________________________________________________________________   Running the model...   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-agents-and-dist-virus-tool.R 2 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 2 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 3 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 4 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 4 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 4 tests [0;32mOK [0m Starting multiple runs (100) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-agents-and-dist-virus-tool.R 4 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 4 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 4 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m _________________________________________________________________________   Running the model...   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 5 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 6 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 6 tests [0;32mOK [0m Starting multiple runs (100) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-agents-and-dist-virus-tool.R 6 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 6 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 6 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 6 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 7 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 7 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 7 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 7 tests [0;32mOK [0m _________________________________________________________________________   Running the model...   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-agents-and-dist-virus-tool.R 7 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 7 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 8 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 9 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 9 tests [0;32mOK [0m   test-agents-and-dist-virus-tool.R 9 tests [0;32mOK [0m Starting multiple runs (100) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.    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[0;32mOK [0m   test-measles-quarantine-errors.R 13 tests [0;32mOK [0m   test-measles-quarantine-errors.R 14 tests [0;32mOK [0m   test-measles-quarantine-errors.R 15 tests [0;32mOK [0m   test-measles-quarantine-errors.R 16 tests [0;32mOK [0m   test-measles-quarantine-errors.R 17 tests [0;32mOK [0m   test-measles-quarantine-errors.R 18 tests [0;32mOK [0m   test-measles-quarantine-errors.R 19 tests [0;32mOK [0m   test-measles-quarantine-errors.R 20 tests [0;32mOK [0m   test-measles-quarantine-errors.R 21 tests [0;32mOK [0m   test-measles-quarantine-errors.R 22 tests [0;32mOK [0m   test-measles-quarantine-errors.R 23 tests [0;32mOK [0m   test-measles-quarantine-errors.R 24 tests [0;32mOK [0m   test-measles-quarantine-errors.R 25 tests [0;32mOK [0m   test-measles-quarantine-errors.R 26 tests [0;32mOK [0m   test-measles-quarantine-errors.R 27 tests [0;32mOK [0m   test-measles-quarantine-errors.R 28 tests [0;32mOK [0m   test-measles-quarantine-errors.R 29 tests [0;32mOK [0m   test-measles-quarantine-errors.R 30 tests [0;32mOK [0m   test-measles-quarantine-errors.R 31 tests [0;32mOK [0m   test-measles-quarantine-errors.R 32 tests [0;32mOK [0m   test-measles-quarantine-errors.R 33 tests [0;32mOK [0m   test-measles-quarantine-errors.R 34 tests [0;32mOK [0m   test-measles-quarantine-errors.R 35 tests [0;32mOK [0m   test-measles-quarantine-errors.R 36 tests [0;32mOK [0m   test-measles-quarantine-errors.R 37 tests [0;32mOK [0m   test-measles-quarantine-errors.R 38 tests [0;32mOK [0m   test-measles-quarantine-errors.R 39 tests [0;32mOK [0m [0;36m85ms [0m      test-measles-quarantine-math.R 0 tests Starting multiple runs (200) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.   ----- PASSED : test-measles-quarantine-math.R<4--39>    call| expect_equal(r0_obs, R0, tolerance = 0.1)   Starting multiple runs (200) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.   ----- PASSED : test-measles-quarantine-math.R<4--39>    call| expect_equal(r0_obs, R0, tolerance = 0.1)   Starting multiple runs (200) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.   ----- PASSED : test-measles-quarantine-math.R<4--39>    call| expect_equal(r0_obs, R0, tolerance = 0.1)      test-measles-quarantine-math.R 3 tests [0;32mOK [0m [0;34m4.1s [0m      test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests _________________________________________________________________________   Running the model...   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-measlesmixing.R.......... 0 tests ________________________________________________________________________________   ________________________________________________________________________________   SIMULATION STUDY      Name of the model : Measles with Mixing and Quarantine   Population size : 9000   Agents' data : (none)   Number of entities : 3   Days (duration) : 100 (of 100)   Number of viruses : 1   Last run elapsed t : 49.00ms   Last run speed : 18.10 million agents x day / second   Rewiring : off      Global events:    - Update infected individuals (runs daily)      Virus(es):    - Measles      Tool(s):    - Vaccine      Model parameters:    - (IGNORED) Vax improved recovery : 0.8000    - Contact rate : 15.0000    - Contact tracing days prior : 4.0000    - Contact tracing success rate : 0.8000    - Days undetected : 2.0000    - Hospitalization period : 10.0000    - Hospitalization rate : 0.1000    - Incubation period : 10.0000    - Isolation period : 10.0000    - Isolation willingness : 0.8000    - Prodromal period : 3.0000    - Quarantine period : 14.0000    - Quarantine willingness : 0.9000    - Rash period : 7.0000    - Transmission rate : 0.9000    - Vaccination rate : 0.9500    - Vax efficacy : 0.9700      Distribution of the population at time 100:     - ( 0) Susceptible : 8999 -> 8999     - ( 1) Exposed : 1 -> 0     - ( 2) Prodromal : 0 -> 0     - ( 3) Rash : 0 -> 0     - ( 4) Isolated : 0 -> 0     - ( 5) Isolated Recovered : 0 -> 0     - ( 6) Detected Hospitalized : 0 -> 0     - ( 7) Quarantined Exposed : 0 -> 0     - ( 8) Quarantined Susceptible : 0 -> 0     - ( 9) Quarantined Prodromal : 0 -> 0     - (10) Quarantined Recovered : 0 -> 0     - (11) Hospitalized : 0 -> 0     - (12) Recovered : 0 -> 1      Transition Probabilities:    - Susceptible 1.00 0.00 - - - - - - - - - - -    - Exposed - 0.96 0.04 - - - - - - - - - -    - Prodromal - - - 1.00 - - - - - - - - -    - Rash - - - - - 1.00 - - - - - - -    - Isolated - - - - - - - - - - - - -    - Isolated Recovered - - - - - 0.89 - - - - - - 0.11    - Detected Hospitalized - - - - - - - - - - - - -    - Quarantined Exposed - - - - - - - - - - - - -    - Quarantined Susceptible - - - - - - - - - - - - -    - Quarantined Prodromal - - - - - - - - - - - - -    - Quarantined Recovered - - - - - - - - - - - - -    - Hospitalized - - - - - - - - - - - - -    - Recovered - - - - - - - - - - - - 1.00         test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 0 tests   test-measlesmixing.R.......... 1 tests [0;32mOK [0m   test-measlesmixing.R.......... 2 tests [0;32mOK [0m   test-measlesmixing.R.......... 3 tests [0;32mOK [0m   test-measlesmixing.R.......... 4 tests [0;32mOK [0m   test-measlesmixing.R.......... 5 tests [0;32mOK [0m   test-measlesmixing.R.......... 6 tests [0;32mOK [0m   test-measlesmixing.R.......... 7 tests [0;32mOK [0m   test-measlesmixing.R.......... 8 tests [0;32mOK [0m [0;34m0.1s [0m      test-measlesmixingriskquarantine-multiple.R 0 tests   test-measlesmixingriskquarantine-multiple.R 0 tests   test-measlesmixingriskquarantine-multiple.R 0 tests   test-measlesmixingriskquarantine-multiple.R 0 tests   test-measlesmixingriskquarantine-multiple.R 0 tests   test-measlesmixingriskquarantine-multiple.R 0 tests   test-measlesmixingriskquarantine-multiple.R 0 tests   test-measlesmixingriskquarantine-multiple.R 0 tests   test-measlesmixingriskquarantine-multiple.R 0 tests   test-measlesmixingriskquarantine-multiple.R 0 tests Starting multiple runs (50) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-measlesmixingriskquarantine-multiple.R 0 tests Starting multiple runs (50) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-measlesmixingriskquarantine-multiple.R 0 tests Starting multiple runs (50) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-measlesmixingriskquarantine-multiple.R 0 tests Starting multiple runs (50) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-measlesmixingriskquarantine-multiple.R 0 tests Starting multiple runs (50) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-measlesmixingriskquarantine-multiple.R 0 tests   test-measlesmixingriskquarantine-multiple.R 1 tests [0;32mOK [0m   test-measlesmixingriskquarantine-multiple.R 2 tests [0;32mOK [0m   test-measlesmixingriskquarantine-multiple.R 3 tests [0;32mOK [0m   test-measlesmixingriskquarantine-multiple.R 4 tests [0;32mOK [0m   test-measlesmixingriskquarantine-multiple.R 5 tests [0;32mOK [0m   test-measlesmixingriskquarantine-multiple.R 6 tests [0;32mOK [0m   test-measlesmixingriskquarantine-multiple.R 7 tests [0;32mOK [0m [0;34m2.1s [0m      test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests _________________________________________________________________________   Running the model...   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-measlesmixingriskquarantine.R 0 tests ________________________________________________________________________________   ________________________________________________________________________________   SIMULATION STUDY      Name of the model : Measles with Mixing and Risk-based Quarantine   Population size : 9000   Agents' data : (none)   Number of entities : 3   Days (duration) : 100 (of 100)   Number of viruses : 1   Last run elapsed t : 46.00ms   Last run speed : 19.16 million agents x day / second   Rewiring : off      Global events:    - Update infected individuals (runs daily)      Virus(es):    - Measles      Tool(s):    - Vaccine      Model parameters:    - Contact rate : 15.0000    - Contact tracing days prior : 4.0000    - Contact tracing success rate : 0.8000    - Days undetected : 2.0000    - Detection rate quarantine : 0.5000    - Hospitalization period : 10.0000    - Hospitalization rate : 0.1000    - Incubation period : 10.0000    - Isolation period : 10.0000    - Isolation willingness : 0.8000    - Prodromal period : 3.0000    - Quarantine period high : 21.0000    - Quarantine period low : 7.0000    - Quarantine period medium : 14.0000    - Quarantine willingness : 0.9000    - Rash period : 7.0000    - Transmission rate : 0.9000    - Vaccination rate : 0.9500    - Vax efficacy : 0.9700      Distribution of the population at time 100:     - ( 0) Susceptible : 8999 -> 8999     - ( 1) Exposed : 1 -> 0     - ( 2) Prodromal : 0 -> 0     - ( 3) Rash : 0 -> 0     - ( 4) Isolated : 0 -> 0     - ( 5) Isolated Recovered : 0 -> 0     - ( 6) Detected Hospitalized : 0 -> 0     - ( 7) Quarantined Exposed : 0 -> 0     - ( 8) Quarantined Susceptible : 0 -> 0     - ( 9) Quarantined Prodromal : 0 -> 0     - (10) Quarantined Recovered : 0 -> 0     - (11) Hospitalized : 0 -> 0     - (12) Recovered : 0 -> 1      Transition Probabilities:    - Susceptible 1.00 0.00 - - - - - - 0.00 - - - -    - Exposed - 0.96 0.04 - - - - - - - - - -    - Prodromal - - - 1.00 - - - - - - - - -    - Rash - - - - - 1.00 - - - - - - -    - Isolated - - - - - - - - - - - - -    - Isolated Recovered - - - - - 0.89 - - - - - - 0.11    - Detected Hospitalized - - - - - - - - - - - - -    - Quarantined Exposed - - - - - - - - - - - - -    - Quarantined Susceptible 0.09 - - - - - - - 0.91 - - - -    - Quarantined Prodromal - - - - - - - - - - - - -    - Quarantined Recovered - - - - - - - - - - - - -    - Hospitalized - - - - - - - - - - - - -    - Recovered - - - - - - - - - - - - 1.00         test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 0 tests   test-measlesmixingriskquarantine.R 1 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 2 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 3 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 4 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 5 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 6 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 7 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 8 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 9 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 10 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 11 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 12 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 13 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 14 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 15 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 16 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 17 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 18 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 19 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 20 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 21 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 22 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 23 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 24 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 25 tests [0;32mOK [0m   test-measlesmixingriskquarantine.R 26 tests [0;32mOK [0m [0;34m0.1s [0m      test-model-diagram.R.......... 0 tests   test-model-diagram.R.......... 0 tests   test-model-diagram.R.......... 0 tests   test-model-diagram.R.......... 0 tests   test-model-diagram.R.......... 1 tests [0;32mOK [0m   test-model-diagram.R.......... 2 tests [0;32mOK [0m   test-model-diagram.R.......... 3 tests [0;32mOK [0m   test-model-diagram.R.......... 4 tests [0;32mOK [0m   test-model-diagram.R.......... 5 tests [0;32mOK [0m   test-model-diagram.R.......... 6 tests [0;32mOK [0m   test-model-diagram.R.......... 7 tests [0;32mOK [0m   test-model-diagram.R.......... 8 tests [0;32mOK [0m   test-model-diagram.R.......... 9 tests [0;32mOK [0m   test-model-diagram.R.......... 10 tests [0;32mOK [0m   test-model-diagram.R.......... 11 tests [0;32mOK [0m   test-model-diagram.R.......... 12 tests [0;32mOK [0m   test-model-diagram.R.......... 12 tests [0;32mOK [0m   test-model-diagram.R.......... 13 tests [0;32mOK [0m   test-model-diagram.R.......... 14 tests [0;32mOK [0m   test-model-diagram.R.......... 15 tests [0;32mOK [0m   test-model-diagram.R.......... 16 tests [0;32mOK [0m   test-model-diagram.R.......... 17 tests [0;32mOK [0m   test-model-diagram.R.......... 18 tests [0;32mOK [0m   test-model-diagram.R.......... 18 tests [0;32mOK [0m   test-model-diagram.R.......... 19 tests [0;32mOK [0m   test-model-diagram.R.......... 19 tests [0;32mOK [0m   test-model-diagram.R.......... 20 tests [0;32mOK [0m   test-model-diagram.R.......... 21 tests [0;32mOK [0m   test-model-diagram.R.......... 22 tests [0;32mOK [0m   test-model-diagram.R.......... 23 tests [0;32mOK [0m   test-model-diagram.R.......... 24 tests [0;32mOK [0m   test-model-diagram.R.......... 25 tests [0;32mOK [0m   test-model-diagram.R.......... 25 tests [0;32mOK [0m   test-model-diagram.R.......... 26 tests [0;32mOK [0m   test-model-diagram.R.......... 27 tests [0;32mOK [0m   test-model-diagram.R.......... 28 tests [0;32mOK [0m   test-model-diagram.R.......... 29 tests [0;32mOK [0m   test-model-diagram.R.......... 30 tests [0;32mOK [0m   test-model-diagram.R.......... 31 tests [0;32mOK [0m   test-model-diagram.R.......... 31 tests [0;32mOK [0m   test-model-diagram.R.......... 32 tests [0;32mOK [0m   test-model-diagram.R.......... 32 tests [0;32mOK [0m   test-model-diagram.R.......... 33 tests [0;32mOK [0m   test-model-diagram.R.......... 34 tests [0;32mOK [0m   test-model-diagram.R.......... 35 tests [0;32mOK [0m   test-model-diagram.R.......... 36 tests [0;32mOK [0m   test-model-diagram.R.......... 37 tests [0;32mOK [0m   test-model-diagram.R.......... 38 tests [0;32mOK [0m   test-model-diagram.R.......... 39 tests [0;32mOK [0m   test-model-diagram.R.......... 40 tests [0;32mOK [0m   test-model-diagram.R.......... 41 tests [0;32mOK [0m [0;34m0.1s [0m      test-model-methods.R.......... 0 tests   test-model-methods.R.......... 0 tests   test-model-methods.R.......... 0 tests   test-model-methods.R.......... 1 tests [0;32mOK [0m   test-model-methods.R.......... 2 tests [0;32mOK [0m   test-model-methods.R.......... 3 tests [0;31m1 fails [0m   test-model-methods.R.......... 4 tests [0;31m2 fails [0m   test-model-methods.R.......... 4 tests [0;31m2 fails [0m   test-model-methods.R.......... 5 tests [0;31m2 fails [0m   test-model-methods.R.......... 6 tests [0;31m2 fails [0m   test-model-methods.R.......... 7 tests [0;31m2 fails [0m   test-model-methods.R.......... 8 tests [0;31m2 fails [0m   test-model-methods.R.......... 9 tests [0;31m2 fails [0m [0;36m86ms [0m      test-multiple.R............... 0 tests   test-multiple.R............... 0 tests   test-multiple.R............... 0 tests   test-multiple.R............... 0 tests _________________________________________________________________________   |Running the model...   |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.   |   test-multiple.R............... 0 tests   test-multiple.R............... 0 tests Starting multiple runs (50) using 2 thread(s)   _________________________________________________________________________   _________________________________________________________________________   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-multiple.R............... 0 tests   test-multiple.R............... 0 tests   test-multiple.R............... 0 tests   test-multiple.R............... 0 tests   test-multiple.R............... 0 tests   test-multiple.R............... 1 tests [0;32mOK [0m   test-multiple.R............... 2 tests [0;32mOK [0m [0;34m4.3s [0m      test-seir.R................... 1 tests [0;32mOK [0m   test-seir.R................... 2 tests [0;32mOK [0m   test-seir.R................... 3 tests [0;32mOK [0m   test-seir.R................... 4 tests [0;32mOK [0m   test-seir.R................... 5 tests [0;32mOK [0m   test-seir.R................... 6 tests [0;32mOK [0m   test-seir.R................... 7 tests [0;32mOK [0m   test-seir.R................... 8 tests [0;32mOK [0m   test-seir.R................... 9 tests [0;32mOK [0m   test-seir.R................... 10 tests [0;32mOK [0m   test-seir.R................... 11 tests [0;32mOK [0m   test-seir.R................... 11 tests [0;32mOK [0m   test-seir.R................... 12 tests [0;32mOK [0m   test-seir.R................... 13 tests [0;32mOK [0m   test-seir.R................... 14 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 15 tests [0;32mOK [0m   test-seir.R................... 16 tests [0;32mOK [0m 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tests [0;32mOK [0m   test-seirconn.R............... 4 tests [0;32mOK [0m   test-seirconn.R............... 4 tests [0;32mOK [0m   test-seirconn.R............... 4 tests [0;32mOK [0m   test-seirconn.R............... 4 tests [0;32mOK [0m   test-seirconn.R............... 4 tests [0;32mOK [0m   test-seirconn.R............... 4 tests [0;32mOK [0m   test-seirconn.R............... 5 tests [0;32mOK [0m   test-seirconn.R............... 6 tests [0;32mOK [0m   test-seirconn.R............... 7 tests [0;32mOK [0m   test-seirconn.R............... 8 tests [0;32mOK [0m   test-seirconn.R............... 9 tests [0;32mOK [0m   test-seirconn.R............... 10 tests [0;32mOK [0m   test-seirconn.R............... 11 tests [0;32mOK [0m   test-seirconn.R............... 12 tests [0;32mOK [0m   test-seirconn.R............... 13 tests [0;32mOK [0m   test-seirconn.R............... 14 tests [0;32mOK [0m   test-seirconn.R............... 15 tests [0;32mOK [0m   test-seirconn.R............... 16 tests [0;32mOK [0m   test-seirconn.R............... 17 tests [0;32mOK [0m   test-seirconn.R............... 18 tests [0;32mOK [0m [0;36m10ms [0m      test-seird.R.................. 0 tests   test-seird.R.................. 0 tests   test-seird.R.................. 0 tests   test-seird.R.................. 0 tests   test-seird.R.................. 0 tests   test-seird.R.................. 0 tests   test-seird.R.................. 1 tests [0;32mOK [0m   test-seird.R.................. 2 tests [0;32mOK [0m   test-seird.R.................. 3 tests [0;32mOK [0m   test-seird.R.................. 4 tests [0;32mOK [0m   test-seird.R.................. 4 tests [0;32mOK [0m   test-seird.R.................. 4 tests [0;32mOK [0m   test-seird.R.................. 4 tests [0;32mOK [0m   test-seird.R.................. 4 tests [0;32mOK [0m   test-seird.R.................. 4 tests [0;32mOK [0m   test-seird.R.................. 5 tests [0;32mOK [0m   test-seird.R.................. 6 tests [0;32mOK [0m   test-seird.R.................. 7 tests [0;32mOK [0m   test-seird.R.................. 8 tests [0;32mOK [0m   test-seird.R.................. 9 tests [0;32mOK [0m   test-seird.R.................. 10 tests [0;32mOK [0m   test-seird.R.................. 11 tests [0;32mOK [0m   test-seird.R.................. 12 tests [0;32mOK [0m   test-seird.R.................. 13 tests [0;32mOK [0m   test-seird.R.................. 14 tests [0;32mOK [0m   test-seird.R.................. 15 tests [0;32mOK [0m   test-seird.R.................. 16 tests [0;32mOK [0m [0;36m12ms [0m      test-seirdconn.R.............. 0 tests   test-seirdconn.R.............. 0 tests   test-seirdconn.R.............. 0 tests   test-seirdconn.R.............. 0 tests   test-seirdconn.R.............. 0 tests   test-seirdconn.R.............. 0 tests   test-seirdconn.R.............. 0 tests   test-seirdconn.R.............. 0 tests   test-seirdconn.R.............. 1 tests [0;32mOK [0m   test-seirdconn.R.............. 2 tests [0;32mOK [0m   test-seirdconn.R.............. 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  test-seirdconn.R.............. 16 tests [0;32mOK [0m   test-seirdconn.R.............. 17 tests [0;32mOK [0m   test-seirdconn.R.............. 18 tests [0;32mOK [0m   test-seirdconn.R.............. 19 tests [0;32mOK [0m   test-seirdconn.R.............. 20 tests [0;32mOK [0m [0;36m13ms [0m      test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests _________________________________________________________________________   Running the model...   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-seirmixing.R............. 0 tests ________________________________________________________________________________   ________________________________________________________________________________   SIMULATION STUDY      Name of the model : Susceptible-Exposed-Infected-Removed (SEIR) with Mixing   Population size : 9000   Agents' data : (none)   Number of entities : 3   Days (duration) : 100 (of 100)   Number of viruses : 1   Last run elapsed t : 96.00ms   Last run speed : 9.29 million agents x day / second   Rewiring : off      Global events:    - Update infected individuals (runs daily)      Virus(es):    - Flu      Tool(s):    (none)      Model parameters:    - Avg. Incubation days : 0.0090    - Contact rate : 40.0000    - Prob. Recovery : 0.1000    - Prob. Transmission : 1.0000      Distribution of the population at time 100:     - (0) Susceptible : 8999 -> 6000     - (1) Exposed : 1 -> 0     - (2) Infected : 0 -> 0     - (3) Recovered : 0 -> 3000      Transition Probabilities:    - Susceptible 1.00 0.00 - -    - Exposed - - 1.00 -    - Infected - - 0.90 0.10    - Recovered - - - 1.00         test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 0 tests   test-seirmixing.R............. 1 tests [0;32mOK [0m   test-seirmixing.R............. 2 tests [0;32mOK [0m   test-seirmixing.R............. 3 tests [0;32mOK [0m   test-seirmixing.R............. 4 tests [0;32mOK [0m   test-seirmixing.R............. 5 tests [0;32mOK [0m   test-seirmixing.R............. 6 tests [0;32mOK [0m   test-seirmixing.R............. 7 tests [0;32mOK [0m   test-seirmixing.R............. 8 tests [0;32mOK [0m   test-seirmixing.R............. 9 tests [0;32mOK [0m   test-seirmixing.R............. 10 tests [0;32mOK [0m   test-seirmixing.R............. 11 tests [0;32mOK [0m   test-seirmixing.R............. 12 tests [0;32mOK [0m   test-seirmixing.R............. 13 tests [0;32mOK [0m   test-seirmixing.R............. 14 tests [0;32mOK [0m   test-seirmixing.R............. 15 tests [0;32mOK [0m   test-seirmixing.R............. 16 tests [0;32mOK [0m [0;34m0.2s [0m      test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests _________________________________________________________________________   Running the model...   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.      test-seirmixingquarantine.R... 0 tests ________________________________________________________________________________   ________________________________________________________________________________   SIMULATION STUDY      Name of the model : SEIR with Mixing and Quarantine   Population size : 9000   Agents' data : (none)   Number of entities : 3   Days (duration) : 100 (of 100)   Number of viruses : 1   Last run elapsed t : 77.00ms   Last run speed : 11.55 million agents x day / second   Rewiring : off      Global events:    - Update infected individuals (runs daily)      Virus(es):    - Flu      Tool(s):    (none)      Model parameters:    - Avg. Incubation days : 0.0090    - Contact rate : 40.0000    - Contact tracing days prior : 3.0000    - Contact tracing success rate : 0.7000    - Days undetected : 3.0000    - Hospitalization period : 7.0000    - Hospitalization rate : 0.0500    - Isolation period : 7.0000    - Isolation willingness : 0.5000    - Prob. Recovery : 0.1000    - Prob. Transmission : 1.0000    - Quarantine period : 14.0000    - Quarantine willingness : 0.8000      Distribution of the population at time 100:     - ( 0) Susceptible : 8999 -> 6000     - ( 1) Exposed : 1 -> 0     - ( 2) Infected : 0 -> 0     - ( 3) Isolated : 0 -> 0     - ( 4) Detected Hospitalized : 0 -> 0     - ( 5) Quarantined Susceptible : 0 -> 0     - ( 6) Quarantined Exposed : 0 -> 0     - ( 7) Isolated Recovered : 0 -> 0     - ( 8) Hospitalized : 0 -> 0     - ( 9) Recovered : 0 -> 3000      Transition Probabilities:    - Susceptible 1.00 0.00 - - - - 0.00 - - -    - Exposed - - 0.92 0.08 - - - - - -    - Infected - - 0.73 0.11 0.02 - - 0.01 0.03 0.09    - Isolated - - 0.15 0.71 0.04 - - 0.08 0.01 0.02    - Detected Hospitalized - - - - 0.86 - - - - 0.14    - Quarantined Susceptible - - - - - - - - - -    - Quarantined Exposed - - - 1.00 - - - - - -    - Isolated Recovered - - - - - - - 0.72 - 0.28    - Hospitalized - - - - - - - - 0.85 0.15    - Recovered - - - - - - - - - 1.00         test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 0 tests   test-seirmixingquarantine.R... 1 tests [0;32mOK [0m   test-seirmixingquarantine.R... 2 tests [0;32mOK [0m   test-seirmixingquarantine.R... 3 tests [0;32mOK [0m   test-seirmixingquarantine.R... 4 tests [0;32mOK [0m   test-seirmixingquarantine.R... 5 tests 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[0m   test-tool.R................... 10 tests [0;32mOK [0m   test-tool.R................... 11 tests [0;32mOK [0m   test-tool.R................... 12 tests [0;32mOK [0m   test-tool.R................... 13 tests [0;32mOK [0m   test-tool.R................... 14 tests [0;32mOK [0m   test-tool.R................... 15 tests [0;32mOK [0m   test-tool.R................... 16 tests [0;32mOK [0m   test-tool.R................... 17 tests [0;32mOK [0m   test-tool.R................... 18 tests [0;32mOK [0m [0;36m16ms [0m      test-virus.R.................. 1 tests [0;32mOK [0m   test-virus.R.................. 2 tests [0;32mOK [0m   test-virus.R.................. 3 tests [0;32mOK [0m   test-virus.R.................. 4 tests [0;32mOK [0m [0;36m6ms [0m   ----- FAILED[xcpt]: test-model-methods.R<19--22>    call| expect_message(md_with_output <- draw_mermaid(model, output_file = "mermaid_diagram.txt"),    call| --> "Diagram written")    diff| No message was emitted    diff| Found 0 message(s), 0 warning(s), and 1 error(s):    diff|    diff| ERR: Could not open the file mermaid_diagram.txt for writing.   ----- FAILED[data]: test-model-methods.R<25--25>    call| expect_true(file.exists("mermaid_diagram.txt"))    diff| Expected TRUE, got FALSE   Error: 2 out of 511 tests failed   In addition: Warning message:   In file.remove("mermaid_diagram.txt") :     cannot remove file 'mermaid_diagram.txt', reason 'Read-only file system'   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [37s/54s] OK
• checking PDF version of manual ... [13s/18s] OK
• checking HTML version of manual ... [3s/5s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR