CRAN Package Check Results for Maintainer ‘George Vega Yon <g.vegayon at gmail.com>’

Last updated on 2025-11-16 01:49:48 CET.

Package ERROR WARN NOTE OK
ABCoptim 13
epiworldR 2 3 8
ergmito 8 5
fmcmc 2 11
googlePublicData 2 11
netdiffuseR 9 2 2
netplot 13
rgexf 2 11
slurmR 2 11

Package ABCoptim

Current CRAN status: OK: 13

Package epiworldR

Current CRAN status: ERROR: 2, NOTE: 3, OK: 8

Additional issues

rchk

Version: 0.10.0.0
Check: tests
Result: ERROR Running ‘tinytest.R’ [21s/33s] 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 <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 1 tests <1b>[0;32mOK<1b>[0m Starting multiple runs (100) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 1 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 1 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 1 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 1 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m _________________________________________________________________________ Running the model... ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 3 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m Starting multiple runs (100) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m _________________________________________________________________________ Running the model... ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m Starting multiple runs (100) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m _________________________________________________________________________ Running the model... ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 8 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 9 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 9 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 9 tests <1b>[0;32mOK<1b>[0m Starting multiple runs (100) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 9 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 9 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 9 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 10 tests <1b>[0;32mOK<1b>[0m <1b>[0;34m4.3s<1b>[0m test-diffnet.R................ 0 tests test-diffnet.R................ 0 tests test-diffnet.R................ 0 tests test-diffnet.R................ 0 tests test-diffnet.R................ 0 tests test-diffnet.R................ 0 tests test-diffnet.R................ 0 tests test-diffnet.R................ 1 tests <1b>[0;32mOK<1b>[0m test-diffnet.R................ 2 tests <1b>[0;32mOK<1b>[0m test-diffnet.R................ 3 tests <1b>[0;32mOK<1b>[0m test-diffnet.R................ 4 tests <1b>[0;32mOK<1b>[0m test-diffnet.R................ 4 tests <1b>[0;32mOK<1b>[0m test-diffnet.R................ 4 tests <1b>[0;32mOK<1b>[0m 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<1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 13 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 14 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 15 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 16 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 17 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 18 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 19 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 20 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 21 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 22 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 23 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 24 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 25 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 26 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 27 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 28 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 29 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 30 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 31 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 32 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 33 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 34 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 35 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 36 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 37 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 38 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 39 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m36ms<1b>[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 <1b>[0;32mOK<1b>[0m <1b>[0;34m3.3s<1b>[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 : 46.00ms Last run speed : 19.35 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 <1b>[0;32mOK<1b>[0m test-measlesmixing.R.......... 2 tests <1b>[0;32mOK<1b>[0m test-measlesmixing.R.......... 3 tests <1b>[0;32mOK<1b>[0m test-measlesmixing.R.......... 4 tests <1b>[0;32mOK<1b>[0m test-measlesmixing.R.......... 5 tests <1b>[0;32mOK<1b>[0m test-measlesmixing.R.......... 6 tests <1b>[0;32mOK<1b>[0m test-measlesmixing.R.......... 7 tests <1b>[0;32mOK<1b>[0m test-measlesmixing.R.......... 8 tests <1b>[0;32mOK<1b>[0m <1b>[0;34m0.1s<1b>[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 <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine-multiple.R 2 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine-multiple.R 3 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine-multiple.R 4 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine-multiple.R 5 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine-multiple.R 6 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine-multiple.R 7 tests <1b>[0;32mOK<1b>[0m <1b>[0;34m1.6s<1b>[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 : 26.00ms Last run speed : 33.87 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 <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 2 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 3 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 4 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 5 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 6 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 7 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 8 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 9 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 10 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 11 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 12 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 13 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 14 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 15 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 16 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 17 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 18 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 19 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 20 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 21 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 22 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 23 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 24 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 25 tests <1b>[0;32mOK<1b>[0m test-measlesmixingriskquarantine.R 26 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m74ms<1b>[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 <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 2 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 3 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 4 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 5 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 6 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 7 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 8 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 9 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 10 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 11 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 12 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 12 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 13 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 14 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 15 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 16 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 17 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 18 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 18 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 19 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 19 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 20 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 21 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 22 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 23 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 24 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 25 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 25 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 26 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 27 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 28 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 29 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 30 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 31 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 31 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 32 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 32 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 33 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 34 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 35 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 36 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 37 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 38 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 39 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 40 tests <1b>[0;32mOK<1b>[0m test-model-diagram.R.......... 41 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m62ms<1b>[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 <1b>[0;32mOK<1b>[0m test-model-methods.R.......... 2 tests <1b>[0;32mOK<1b>[0m test-model-methods.R.......... 3 tests <1b>[0;31m1 fails<1b>[0m test-model-methods.R.......... 4 tests <1b>[0;31m2 fails<1b>[0m test-model-methods.R.......... 4 tests <1b>[0;31m2 fails<1b>[0m test-model-methods.R.......... 5 tests <1b>[0;31m2 fails<1b>[0m test-model-methods.R.......... 6 tests <1b>[0;31m2 fails<1b>[0m test-model-methods.R.......... 7 tests <1b>[0;31m2 fails<1b>[0m test-model-methods.R.......... 8 tests <1b>[0;31m2 fails<1b>[0m test-model-methods.R.......... 9 tests <1b>[0;31m2 fails<1b>[0m <1b>[0;36m51ms<1b>[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) _________________________________________________________________________ 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test-seirdconn.R.............. 8 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 9 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 10 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 11 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 12 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 13 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 14 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 15 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 16 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 17 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 18 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 19 tests <1b>[0;32mOK<1b>[0m test-seirdconn.R.............. 20 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m11ms<1b>[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 : 70.00ms Last run speed : 12.79 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 <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 2 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 3 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 4 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 5 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 6 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 7 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 8 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 9 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 10 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 11 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 12 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 13 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 14 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 15 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 16 tests <1b>[0;32mOK<1b>[0m <1b>[0;34m0.1s<1b>[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 : 81.00ms Last run speed : 11.00 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 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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 Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.10.0.0
Check: tests
Result: 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 <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 1 tests <1b>[0;32mOK<1b>[0m Starting multiple runs (100) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 1 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 1 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 1 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 1 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m _________________________________________________________________________ Running the model... ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 2 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 3 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m Starting multiple runs (100) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 4 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m _________________________________________________________________________ Running the model... ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 5 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m Starting multiple runs (100) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 6 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m _________________________________________________________________________ Running the model... ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 7 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 8 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 9 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 9 tests <1b>[0;32mOK<1b>[0m test-agents-and-dist-virus-tool.R 9 tests <1b>[0;32mOK<1b>[0m Starting multiple runs (100) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ 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<1b>[0;32mOK<1b>[0m test-diffnet.R................ 10 tests <1b>[0;32mOK<1b>[0m test-diffnet.R................ 11 tests <1b>[0;32mOK<1b>[0m test-diffnet.R................ 12 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m22ms<1b>[0m test-get.R.................... 0 tests test-get.R.................... 0 tests test-get.R.................... 1 tests <1b>[0;32mOK<1b>[0m test-get.R.................... 2 tests <1b>[0;32mOK<1b>[0m test-get.R.................... 3 tests <1b>[0;32mOK<1b>[0m test-get.R.................... 4 tests <1b>[0;32mOK<1b>[0m test-get.R.................... 5 tests <1b>[0;32mOK<1b>[0m test-get.R.................... 6 tests <1b>[0;32mOK<1b>[0m test-get.R.................... 6 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m17ms<1b>[0m test-lfmcmc.R................. 0 tests test-lfmcmc.R................. 0 tests test-lfmcmc.R................. 0 tests test-lfmcmc.R................. 0 tests test-lfmcmc.R................. 0 tests test-lfmcmc.R................. 1 tests <1b>[0;32mOK<1b>[0m 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tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 2 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 3 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 4 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 5 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 6 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 7 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 8 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 9 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 9 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 9 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 9 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 9 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 9 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 10 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 11 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 12 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 13 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 14 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 15 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 16 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 17 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 18 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 19 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 20 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 21 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 22 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 23 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 24 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 25 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 26 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 27 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 28 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 29 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 30 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 31 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 32 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 33 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 34 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 35 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 36 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 37 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 38 tests <1b>[0;32mOK<1b>[0m test-measles-quarantine-errors.R 39 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m85ms<1b>[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 <1b>[0;32mOK<1b>[0m <1b>[0;34m4.1s<1b>[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 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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) _________________________________________________________________________ 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________________________________________________________________________________ ________________________________________________________________________________ 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 <1b>[0;32mOK<1b>[0m 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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 <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 2 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 3 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 4 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 5 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 6 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 7 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 8 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 9 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 10 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 11 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 12 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 13 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 14 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 15 tests <1b>[0;32mOK<1b>[0m test-seirmixing.R............. 16 tests <1b>[0;32mOK<1b>[0m <1b>[0;34m0.2s<1b>[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 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<1b>[0;32mOK<1b>[0m test-sirlogit.R............... 3 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 3 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 3 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 3 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 3 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 3 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 3 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 3 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 4 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 5 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 6 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 7 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 8 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 9 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 10 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 11 tests <1b>[0;32mOK<1b>[0m test-sirlogit.R............... 12 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m33ms<1b>[0m test-sirmixing.R.............. 0 tests test-sirmixing.R.............. 0 tests test-sirmixing.R.............. 0 tests test-sirmixing.R.............. 0 tests test-sirmixing.R.............. 0 tests test-sirmixing.R.............. 0 tests test-sirmixing.R.............. 0 tests test-sirmixing.R.............. 1 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 2 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 3 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 4 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 4 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 4 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 4 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 4 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 4 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 4 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 4 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 5 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 6 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 7 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 8 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 9 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 10 tests <1b>[0;32mOK<1b>[0m test-sirmixing.R.............. 11 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m14ms<1b>[0m test-sis.R.................... 1 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 2 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 3 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 4 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 5 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 6 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 7 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 8 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 9 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 9 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 9 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 9 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 9 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 9 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 9 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 9 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 9 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 10 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 11 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 12 tests <1b>[0;32mOK<1b>[0m test-sis.R.................... 13 tests <1b>[0;32mOK<1b>[0m <1b>[0;34m0.6s<1b>[0m test-sisd.R................... 0 tests test-sisd.R................... 0 tests test-sisd.R................... 0 tests test-sisd.R................... 0 tests test-sisd.R................... 0 tests test-sisd.R................... 1 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 2 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 3 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 4 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 4 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 4 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 4 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 4 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 5 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 6 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 7 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 8 tests <1b>[0;32mOK<1b>[0m test-sisd.R................... 9 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m9ms<1b>[0m test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 0 tests test-surv.R................... 1 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 2 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 3 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 4 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 4 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 4 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 4 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 4 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 5 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 6 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 7 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 8 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 9 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 10 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 11 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 12 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 13 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 14 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 15 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 16 tests <1b>[0;32mOK<1b>[0m test-surv.R................... 17 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m18ms<1b>[0m test-tool.R................... 0 tests test-tool.R................... 1 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 2 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 3 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 4 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 5 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 5 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 6 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 7 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 8 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 8 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 9 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 10 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 11 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 12 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 13 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 14 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 15 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 16 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 17 tests <1b>[0;32mOK<1b>[0m test-tool.R................... 18 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m16ms<1b>[0m test-virus.R.................. 1 tests <1b>[0;32mOK<1b>[0m test-virus.R.................. 2 tests <1b>[0;32mOK<1b>[0m test-virus.R.................. 3 tests <1b>[0;32mOK<1b>[0m test-virus.R.................. 4 tests <1b>[0;32mOK<1b>[0m <1b>[0;36m6ms<1b>[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 Flavor: r-release-linux-x86_64

Version: 0.8.3.0
Check: installed package size
Result: NOTE installed size is 19.6Mb sub-directories of 1Mb or more: doc 1.9Mb libs 15.6Mb Flavor: r-oldrel-macos-arm64

Version: 0.10.0.0
Check: installed package size
Result: NOTE installed size is 22.5Mb sub-directories of 1Mb or more: doc 1.9Mb help 1.3Mb libs 17.9Mb Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package ergmito

Current CRAN status: NOTE: 8, OK: 5

Version: 0.3-1
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: nvertex.Rd: network Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64

Version: 0.3-1
Check: installed package size
Result: NOTE installed size is 5.6Mb sub-directories of 1Mb or more: libs 4.2Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package fmcmc

Current CRAN status: NOTE: 2, OK: 11

Version: 0.5-2
Check: DESCRIPTION meta-information
Result: NOTE Author field differs from that derived from Authors@R Author: ‘George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>), Paul Marjoram [ctb, ths] (<https://orcid.org/0000-0003-0824-7449>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), Fabian Scheipl [rev] (JOSS reviewer, <https://orcid.org/0000-0001-8172-3603>)’ Authors@R: ‘George Vega Yon [aut, cre] (ORCID: <https://orcid.org/0000-0002-3171-0844>), Paul Marjoram [ctb, ths] (ORCID: <https://orcid.org/0000-0003-0824-7449>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), Fabian Scheipl [rev] (what: JOSS reviewer, ORCID: <https://orcid.org/0000-0001-8172-3603>)’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package googlePublicData

Current CRAN status: NOTE: 2, OK: 11

Version: 0.16.1
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘George Vega Yon <g.vegayon@gmail.com>’ Found the following (possibly) invalid file URI: URI: publicdata.google.com From: man/dspl.Rd Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package netdiffuseR

Current CRAN status: WARN: 9, NOTE: 2, OK: 2

Version: 1.23.0
Check: whether package can be installed
Result: WARN Found the following significant warnings: infection.cpp:58:16: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] infection.cpp:162:16: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/netdiffuseR.Rcheck/00install.out’ for details. * used C++ compiler: ‘Debian clang version 21.1.5 (1)’ Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.23.0
Check: Rd files
Result: NOTE checkRd: (-1) diffnet-class.Rd:214-225: Only 3 columns allowed in this table (row 2 has 1) checkRd: (-1) diffnet-class.Rd:214-225: Only 3 columns allowed in this table (row 6 has 1) checkRd: (-1) diffnet-class.Rd:214-225: Only 3 columns allowed in this table (row 7 has 1) Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.23.0
Check: whether package can be installed
Result: WARN Found the following significant warnings: infection.cpp:58:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] infection.cpp:162:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/netdiffuseR.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’ Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.23.0
Check: whether package can be installed
Result: WARN Found the following significant warnings: infection.cpp:58:16: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] infection.cpp:162:16: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See ‘/data/gannet/ripley/R/packages/tests-clang/netdiffuseR.Rcheck/00install.out’ for details. * used C++ compiler: ‘clang version 21.1.5’ Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.23.0
Check: whether package can be installed
Result: WARN Found the following significant warnings: infection.cpp:58:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] infection.cpp:162:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See ‘/data/gannet/ripley/R/packages/tests-devel/netdiffuseR.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.23.0
Flags: --no-vignettes
Check: whether package can be installed
Result: WARN Found the following significant warnings: infection.cpp:58:25: warning: 'bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] infection.cpp:162:25: warning: 'bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See 'd:/Rcompile/CRANpkg/local/4.6/netdiffuseR.Rcheck/00install.out' for details. * used C++ compiler: 'g++.exe (GCC) 14.3.0' Flavor: r-devel-windows-x86_64

Version: 1.23.0
Check: whether package can be installed
Result: WARN Found the following significant warnings: infection.cpp:58:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] infection.cpp:162:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/netdiffuseR.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’ Flavor: r-patched-linux-x86_64

Version: 1.23.0
Check: whether package can be installed
Result: WARN Found the following significant warnings: infection.cpp:58:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] infection.cpp:162:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/netdiffuseR.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’ Flavor: r-release-linux-x86_64

Version: 1.23.0
Flags: --no-vignettes
Check: whether package can be installed
Result: WARN Found the following significant warnings: infection.cpp:58:25: warning: 'bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] infection.cpp:162:25: warning: 'bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See 'd:/Rcompile/CRANpkg/local/4.5/netdiffuseR.Rcheck/00install.out' for details. * used C++ compiler: 'g++.exe (GCC) 14.3.0' Flavor: r-release-windows-x86_64

Version: 1.23.0
Check: installed package size
Result: NOTE installed size is 10.2Mb sub-directories of 1Mb or more: doc 2.4Mb libs 5.9Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 1.23.0
Flags: --no-vignettes
Check: whether package can be installed
Result: WARN Found the following significant warnings: infection.cpp:58:25: warning: 'bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] infection.cpp:162:25: warning: 'bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See 'd:/Rcompile/CRANpkg/local/4.4/netdiffuseR.Rcheck/00install.out' for details. * used C++ compiler: 'g++.exe (GCC) 13.3.0' Flavor: r-oldrel-windows-x86_64

Version: 1.23.0
Flags: --no-vignettes
Check: installed package size
Result: NOTE installed size is 5.7Mb sub-directories of 1Mb or more: doc 2.5Mb libs 1.5Mb Flavor: r-oldrel-windows-x86_64

Package netplot

Current CRAN status: OK: 13

Package rgexf

Current CRAN status: NOTE: 2, OK: 11

Version: 0.16.3
Check: DESCRIPTION meta-information
Result: NOTE Author field differs from that derived from Authors@R Author: ‘George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>), Jorge Fábrega Lacoa [ctb], Joshua Kunst [ctb], Raphaël Velt [cph] (gexf-js library), Gephi Consortium [cph] (GEXF language), Cornelius Fritz [rev] (JOSS reviewer), Jonathan Cardoso Silva [rev] (JOSS reviewer)’ Authors@R: ‘George Vega Yon [aut, cre] (ORCID: <https://orcid.org/0000-0002-3171-0844>), Jorge Fábrega Lacoa [ctb], Joshua Kunst [ctb], Raphaël Velt [cph] (gexf-js library), Gephi Consortium [cph] (GEXF language), Cornelius Fritz [rev] (what: JOSS reviewer), Jonathan Cardoso Silva [rev] (what: JOSS reviewer)’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package slurmR

Current CRAN status: NOTE: 2, OK: 11

Version: 0.5-4
Check: DESCRIPTION meta-information
Result: NOTE Author field differs from that derived from Authors@R Author: ‘George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>), Paul Marjoram [ctb, ths] (<https://orcid.org/0000-0003-0824-7449>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), Michael Schubert [rev] (JOSS reviewer, <https://orcid.org/0000-0002-6862-5221>), Michel Lang [rev] (JOSS reviewer, <https://orcid.org/0000-0001-9754-0393>)’ Authors@R: ‘George Vega Yon [aut, cre] (ORCID: <https://orcid.org/0000-0002-3171-0844>), Paul Marjoram [ctb, ths] (ORCID: <https://orcid.org/0000-0003-0824-7449>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), Michael Schubert [rev] (what: JOSS reviewer, ORCID: <https://orcid.org/0000-0002-6862-5221>), Michel Lang [rev] (what: JOSS reviewer, ORCID: <https://orcid.org/0000-0001-9754-0393>)’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc