• using R Under development (unstable) (2025-12-22 r89219)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 15.2.0
• 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 ‘0.11.0.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] OK
• 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++-15 (Debian 15.2.0-11) 15.2.0’
• 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/0s] 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 ... [6s/8s] 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 ... NOTE File ‘epiworldR/libs/epiworldR.so’:   Found non-API call to R: ‘ATTRIB’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points.
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [6s/9s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [18s/28s] ERROR   Running ‘tinytest.R’ [18s/28s] Running the tests in ‘tests/tinytest.R’ failed. Complete output:   >   > if (requireNamespace("tinytest", quietly = TRUE)) {   + 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   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)   _________________________________________________________________________   _________________________________________________________________________ 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[0;36m54ms [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 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  test-seirdconn.R.............. 14 tests [0;32mOK [0m   test-seirdconn.R.............. 15 tests [0;32mOK [0m   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;36m6ms [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 : 47.00ms   Last run speed : 19.09 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;36m99ms [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 : 39.00ms   Last run speed : 22.80 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 - - 0.90 0.10 - - - - - -    - Infected - - 0.73 0.12 0.02 - - 0.01 0.03 0.09    - Isolated - - 0.14 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 - - - - - - - - 0.86 0.14    - Recovered - - - - - - - - - 1.00    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   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 631 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 ... [21s/26s] OK
• checking PDF version of manual ... [6s/8s] OK
• checking HTML version of manual ... [5s/7s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE