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Type 'q()' to quit R. > library(testthat) > library(epicR) epicR: Using config files from: /data/gannet/ripley/.config/R/epicR/config To reset configs to defaults, use: reset_user_configs() Attaching package: 'epicR' The following object is masked from 'package:stats': simulate > > test_check("epicR") Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model for jurisdiction: CANADA Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: model_events.cpp:680:70: runtime error: index 3 out of bounds for type 'double [3]' #0 0x7bb1930cda66 in event_exacerbation_process(agent*) /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR/src/model_events.cpp:680 #1 0x7bb1930b46c7 in model_run(int) /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR/src/model.cpp:1603 #2 0x7bb193047bbe in _epicR_model_run /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR/src/RcppExports.cpp:144 #3 0x000000751818 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:754 #4 0x0000008e786a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8682 #5 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #6 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #7 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #8 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #9 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #10 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #11 0x000000872f1b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992 #12 0x00000085f496 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #13 0x000000894461 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #14 0x0000008d0e62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #15 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #16 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #17 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #18 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #19 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #20 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #21 0x000000895553 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3973 #22 0x0000008d0e62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #23 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #24 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #25 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #26 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #27 0x00000087a027 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #28 0x00000087a027 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2456 #29 0x000000499ff6 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75 #30 0x000000a964b6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #31 0x0000008de071 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #32 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #33 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #35 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #36 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #37 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #38 0x000000a03788 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #39 0x000000a03788 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #40 0x000000a11afa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #41 0x000000a11b92 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #42 0x000000412fff in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #43 0x7fb1ab412574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #44 0x7fb1ab412627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #45 0x0000004139e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139e4) (BuildId: 99e27ab03b844008739159187c21cd6ef65f16cc) model_events.cpp:680:70: runtime error: index 3 out of bounds for type 'double [3]' #0 0x7bb1930cdbbc in event_exacerbation_process(agent*) /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR/src/model_events.cpp:680 #1 0x7bb1930b46c7 in model_run(int) /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR/src/model.cpp:1603 #2 0x7bb193047bbe in _epicR_model_run /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR/src/RcppExports.cpp:144 #3 0x000000751818 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:754 #4 0x0000008e786a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8682 #5 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #6 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #7 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #8 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #9 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #10 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #11 0x000000872f1b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992 #12 0x00000085f496 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #13 0x000000894461 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #14 0x0000008d0e62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #15 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #16 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #17 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #18 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #19 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #20 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #21 0x000000895553 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3973 #22 0x0000008d0e62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #23 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #24 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #25 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #26 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #27 0x00000087a027 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #28 0x00000087a027 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2456 #29 0x000000499ff6 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75 #30 0x000000a964b6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #31 0x0000008de071 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #32 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #33 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #35 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #36 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #37 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #38 0x000000a03788 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #39 0x000000a03788 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #40 0x000000a11afa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #41 0x000000a11b92 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #42 0x000000412fff in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #43 0x7fb1ab412574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #44 0x7fb1ab412627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #45 0x0000004139e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139e4) (BuildId: 99e27ab03b844008739159187c21cd6ef65f16cc) 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Terminating the session Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model (with custom input parameters) Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: 10% 20% 30% 40% 50% 60% 70% 80% 90% Terminating the session Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model for jurisdiction: CANADA Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Terminating the session Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model (with custom input parameters) Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Terminating the session Terminating the session Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model for jurisdiction: CANADA Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Terminating the session Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model for jurisdiction: CANADA Record mode: record_mode_event (2) Simulating 60000 base agents: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Terminating the session Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model for jurisdiction: CANADA Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Terminating the session Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat test 1: zero all costs Running EPIC model (with custom input parameters) Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: Test passed! Terminating the session test 2: zero all utilities Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model (with custom input parameters) Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: Test passed! Terminating the session test 3: set all utilities to 1 and get one QALY without discount Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model (with custom input parameters) Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: Test passed! Terminating the session test 4: zero mortality (both bg and exac) Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model (with custom input parameters) Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: Test passed! Terminating the session Initializing the session Working directory: /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR.Rcheck/tests/testthat Running EPIC model for jurisdiction: CANADA Record mode: record_mode_none (0) Note: No events will be recorded. Use record_mode_event (2) or record_mode_agent (1) to record events. Simulating 60000 base agents: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Terminating the session [ FAIL 0 | WARN 3 | SKIP 9 | PASS 2372 ] ══ Skipped tests (9) ═══════════════════════════════════════════════════════════ • Core source file not found (7): 'test-config-reload.R:135:3', 'test-config-reload.R:169:3', 'test-seed-reproducibility.R:58:3', 'test-seed-reproducibility.R:90:3', 'test-seed-reproducibility.R:135:3', 'test-seed-reproducibility.R:210:3', 'test-seed-reproducibility.R:242:3' • Input source file not found (1): 'test-config-reload.R:198:3' • Source file not available (1): 'test-input-functions.R:144:3' [ FAIL 0 | WARN 3 | SKIP 9 | PASS 2372 ] > > proc.time() user system elapsed 578.522 22.395 767.979