--- re-building ‘AddingNewCountry.Rmd’ using rmarkdown
--- finished re-building ‘AddingNewCountry.Rmd’

--- re-building ‘BackgroundEPIC.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘BackgroundEPIC.Rmd’

--- re-building ‘GettingStarted.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘GettingStarted.Rmd’

--- re-building ‘InputsOutputsStructure.Rmd’ using rmarkdown
model_events.cpp:680:70: runtime error: index 3 out of bounds for type 'double [3]'
    #0 0x7b6ddaacda66 in event_exacerbation_process(agent*) /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR/src/model_events.cpp:680
    #1 0x7b6ddaab46c7 in model_run(int) /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR/src/model.cpp:1603
    #2 0x7b6ddaa47bbe 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 0x00000088cebe in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #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 0x000000925741 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #18 0x00000086002c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187
    #19 0x000000896f23 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998
    #20 0x000000a964b6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411
    #21 0x0000008de071 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152
    #22 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #23 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #24 0x000000925741 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #25 0x00000086002c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187
    #26 0x000000925741 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #27 0x0000008a8f81 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956
    #28 0x0000008a8f81 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849
    #29 0x0000008e0cdc in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862
    #30 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #31 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #32 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #33 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #34 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #35 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #36 0x000000894461 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #37 0x0000008d0e62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132
    #38 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #39 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #40 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #41 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #42 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #43 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #44 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #45 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #46 0x0000008e5965 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #47 0x0000008e5965 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103
    #48 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #49 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #50 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #51 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #52 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #53 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #54 0x000000a03788 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #55 0x000000a03788 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317
    #56 0x000000a11afa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235
    #57 0x000000a11b92 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242
    #58 0x000000412fff in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #59 0x7f6df5212574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1)
    #60 0x7f6df5212627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1)
    #61 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 0x7b6ddaacdbbc in event_exacerbation_process(agent*) /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR/src/model_events.cpp:680
    #1 0x7b6ddaab46c7 in model_run(int) /data/gannet/ripley/R/packages/tests-gcc-SAN/epicR/src/model.cpp:1603
    #2 0x7b6ddaa47bbe 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 0x00000088cebe in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #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 0x000000925741 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #18 0x00000086002c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187
    #19 0x000000896f23 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998
    #20 0x000000a964b6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411
    #21 0x0000008de071 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152
    #22 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #23 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #24 0x000000925741 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #25 0x00000086002c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187
    #26 0x000000925741 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #27 0x0000008a8f81 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956
    #28 0x0000008a8f81 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849
    #29 0x0000008e0cdc in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862
    #30 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #31 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #32 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #33 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #34 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #35 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #36 0x000000894461 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #37 0x0000008d0e62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132
    #38 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #39 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #40 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #41 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #42 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #43 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #44 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #45 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #46 0x0000008e5965 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #47 0x0000008e5965 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103
    #48 0x0000008be0ab in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #49 0x00000085e9d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #50 0x00000087471a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #51 0x00000087870a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #52 0x00000085f073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #53 0x00000085f073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #54 0x000000a03788 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #55 0x000000a03788 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317
    #56 0x000000a11afa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235
    #57 0x000000a11b92 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242
    #58 0x000000412fff in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #59 0x7f6df5212574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1)
    #60 0x7f6df5212627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1)
    #61 0x0000004139e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139e4) (BuildId: 99e27ab03b844008739159187c21cd6ef65f16cc)

--- finished re-building ‘InputsOutputsStructure.Rmd’