--- re-building ‘cea.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/ceplane_plot-1.png 768x432 pixels, 3x8 bits/pixel, RGB Input IDAT size = 60857 bytes Input file size = 61019 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44365 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44365 Output IDAT size = 44365 bytes (16492 bytes decrease) Output file size = 44443 bytes (16576 bytes = 27.17% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/mce_plot-1.png 768x432 pixels, 3x8 bits/pixel, RGB Input IDAT size = 41845 bytes Input file size = 41983 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35070 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35070 Output IDAT size = 35070 bytes (6775 bytes decrease) Output file size = 35148 bytes (6835 bytes = 16.28% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/ceac_plot-1.png 768x432 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37929 bytes Input file size = 38055 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32699 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32699 Output IDAT size = 32699 bytes (5230 bytes decrease) Output file size = 32777 bytes (5278 bytes = 13.87% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/ceaf_plot-1.png 768x432 pixels, 3x8 bits/pixel, RGB Input IDAT size = 32612 bytes Input file size = 32726 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27476 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27476 Output IDAT size = 27476 bytes (5136 bytes decrease) Output file size = 27554 bytes (5172 bytes = 15.80% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/evpi_plot-1.png 768x432 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 14199 bytes Input file size = 15069 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12323 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 12298 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 12298 Output IDAT size = 12298 bytes (1901 bytes decrease) Output file size = 12376 bytes (2693 bytes = 17.87% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/totevpi-1.png 576x432 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8270 bytes Input file size = 9140 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7259 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7148 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7148 Output IDAT size = 7148 bytes (1122 bytes decrease) Output file size = 7226 bytes (1914 bytes = 20.94% decrease) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘cea.Rmd’ --- re-building ‘intro.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/intro_files/figure-html/ceac_plot-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24537 bytes Input file size = 24639 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19031 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19031 Output IDAT size = 19031 bytes (5506 bytes decrease) Output file size = 19109 bytes (5530 bytes = 22.44% decrease) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘intro.Rmd’ --- re-building ‘markov-cohort.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/markov-cohort_files/figure-html/simStateprobsPlot-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 77071 bytes Input file size = 77257 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63547 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63547 Output IDAT size = 63547 bytes (13524 bytes decrease) Output file size = 63625 bytes (13632 bytes = 17.65% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/markov-cohort_files/figure-html/ceac-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 23588 bytes Input file size = 23690 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19142 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19142 Output IDAT size = 19142 bytes (4446 bytes decrease) Output file size = 19220 bytes (4470 bytes = 18.87% decrease) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘markov-cohort.Rmd’ --- re-building ‘markov-inhomogeneous-cohort.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/markov-inhomogeneous-cohort_files/figure-html/simStateprobsPlot-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 46353 bytes Input file size = 46491 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36318 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36318 Output IDAT size = 36318 bytes (10035 bytes decrease) Output file size = 36396 bytes (10095 bytes = 21.71% decrease) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘markov-inhomogeneous-cohort.Rmd’ --- re-building ‘markov-inhomogeneous-indiv.Rmd’ using rmarkdown ================================================================= ==452793==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7b8ecf82e540 at pc 0x7b5ebb66af40 bp 0x7ffd3d41ce30 sp 0x7ffd3d41ce28 READ of size 8 at 0x7b8ecf82e540 thread T0 #0 0x7b5ebb66af3f in hesim::stats::piecewise_exponential::piecewise_exponential(std::__1::vector>, std::__1::vector>) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/stats/distributions.h:325:36 #1 0x7b5ebb6694ce in hesim::statmods::surv::init_dist_(hesim::statmods::params_surv) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/statmods/statmods.h:173:15 #2 0x7b5ebb6602e0 in hesim::statmods::surv::surv(std::__1::vector, std::__1::allocator>>, hesim::statmods::params_surv) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/statmods/statmods.h:223:30 #3 0x7b5ebb655b90 in hesim::ctstm::mstate_list::init_survmods_(Rcpp::Environment_Impl) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/ctstm/ctstm.h:187:22 #4 0x7b5ebb654666 in hesim::ctstm::mstate_list::mstate_list(Rcpp::Environment_Impl) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/ctstm/ctstm.h:200:15 #5 0x7b5ebb653843 in hesim::ctstm::transmod::create(Rcpp::Environment_Impl) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/ctstm/ctstm.h:238:15 #6 0x7b5ebb82a6d0 in C_ctstm_sim_disease(Rcpp::Environment_Impl, std::__1::vector>, std::__1::vector>, std::__1::vector>, int, std::__1::basic_string, std::__1::allocator>, std::__1::vector>, std::__1::vector>, double, double, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/indiv-ctstm.cpp:33:54 #7 0x7b5ebb618130 in _hesim_C_ctstm_sim_disease /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/RcppExports.cpp:206:34 #8 0x556b98b80042 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #9 0x556b98b8c5ac in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11 #10 0x556b98c37789 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114:14 #11 0x556b98c2a444 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #12 0x556b98c2896a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #13 0x556b98c708fc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #14 0x556b98c6fac1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #15 0x556b98c293b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #16 0x556b98c293b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #17 0x556b98c81fe7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563:8 #18 0x556b98c28eb3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #19 0x556b98c7f169 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992:10 #20 0x556b98c28eb3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #21 0x556b98c708fc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #22 0x556b98c6fac1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #23 0x556b98c293b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #24 0x556b98c293b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #25 0x556b98c8214c in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3384:5 #26 0x556b98c8214c in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3573:9 #27 0x556b98c28eb3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #28 0x556b98c7f169 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992:10 #29 0x556b98c28eb3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #30 0x556b98c708fc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #31 0x556b98c6fac1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #32 0x556b98c293b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #33 0x556b98c293b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #34 0x556b98c868f3 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937:13 #35 0x556b98c37789 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114:14 #36 0x556b98c2a444 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #37 0x556b98c2896a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #38 0x556b98c2ad01 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #39 0x556b98c28b64 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187:6 #40 0x556b98c87b23 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980:9 #41 0x556b98d32f49 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411:11 #42 0x556b98c3cf83 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134:15 #43 0x556b98c2a444 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #44 0x556b98c2896a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #45 0x556b98c2ad01 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #46 0x556b98c28b64 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187:6 #47 0x556b98c2ad01 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #48 0x556b98c54b37 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831:6 #49 0x556b98c54b37 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844:20 #50 0x556b98c2a444 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #51 0x556b98c2896a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #52 0x556b98c708fc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #53 0x556b98c6fac1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #54 0x556b98c293b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #55 0x556b98c293b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #56 0x556b98c868f3 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937:13 #57 0x556b98c37789 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114:14 #58 0x556b98c2a444 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #59 0x556b98c2896a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x556b98c708fc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #61 0x556b98c6fac1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #62 0x556b98c293b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #63 0x556b98c293b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #64 0x556b98c708fc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #65 0x556b98c6fac1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #66 0x556b98c4d803 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #67 0x556b98c4d803 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085:16 #68 0x556b98c2a444 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #69 0x556b98c2896a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #70 0x556b98c708fc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #71 0x556b98c6fac1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #72 0x556b98c293b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #73 0x556b98c293b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #74 0x556b98cfd1f1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:15 #75 0x556b98cffa40 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #76 0x556b98cffa40 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #77 0x556b98cffad2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #78 0x556b98a0699c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #79 0x7f5ed2f135f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #80 0x7f5ed2f136a7 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #81 0x556b9891f7d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7b8ecf82e540 is located 0 bytes after 32-byte region [0x7b8ecf82e520,0x7b8ecf82e540) allocated by thread T0 here: #0 0x556b989c3f14 in malloc /data/gannet/ripley/Sources2/LLVM/21/latest/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x7f5ed0a1f2fb in operator new(unsigned long) (/lib64/libstdc++.so.6+0x1f2fb) (BuildId: a34f3756a2aefc3d2b7ae49335dfdd1b4555be43) #2 0x7b5ebb66abce in void std::__1::vector>::assign[abi:ne210101](double*, double*) /usr/local/clang21/bin/../include/c++/v1/__vector/vector.h:320:5 #3 0x7b5ebb66abce in std::__1::vector>::operator=[abi:ne210101](std::__1::vector> const&) /usr/local/clang21/bin/../include/c++/v1/__vector/vector.h:1033:5 #4 0x7b5ebb66abce in hesim::stats::piecewise_exponential::piecewise_exponential(std::__1::vector>, std::__1::vector>) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/stats/distributions.h:321:11 #5 0x7b5ebb6694ce in hesim::statmods::surv::init_dist_(hesim::statmods::params_surv) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/statmods/statmods.h:173:15 #6 0x7b5ebb6602e0 in hesim::statmods::surv::surv(std::__1::vector, std::__1::allocator>>, hesim::statmods::params_surv) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/statmods/statmods.h:223:30 #7 0x7b5ebb655b90 in hesim::ctstm::mstate_list::init_survmods_(Rcpp::Environment_Impl) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/ctstm/ctstm.h:187:22 #8 0x7b5ebb654666 in hesim::ctstm::mstate_list::mstate_list(Rcpp::Environment_Impl) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/ctstm/ctstm.h:200:15 #9 0x7b5ebb653843 in hesim::ctstm::transmod::create(Rcpp::Environment_Impl) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/ctstm/ctstm.h:238:15 #10 0x7b5ebb82a6d0 in C_ctstm_sim_disease(Rcpp::Environment_Impl, std::__1::vector>, std::__1::vector>, std::__1::vector>, int, std::__1::basic_string, std::__1::allocator>, std::__1::vector>, std::__1::vector>, double, double, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/indiv-ctstm.cpp:33:54 #11 0x7b5ebb618130 in _hesim_C_ctstm_sim_disease /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/RcppExports.cpp:206:34 #12 0x556b98b80042 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #13 0x556b98b8c5ac in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11 #14 0x556b98c37789 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114:14 #15 0x556b98c2a444 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #16 0x556b98c2896a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #17 0x556b98c708fc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #18 0x556b98c6fac1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #19 0x556b98c293b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #20 0x556b98c293b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #21 0x556b98c81fe7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563:8 #22 0x556b98c28eb3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #23 0x556b98c7f169 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992:10 #24 0x556b98c28eb3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #25 0x556b98c708fc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #26 0x556b98c6fac1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #27 0x556b98c293b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #28 0x556b98c293b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #29 0x556b98c8214c in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3384:5 #30 0x556b98c8214c in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3573:9 #31 0x556b98c28eb3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #32 0x556b98c7f169 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992:10 #33 0x556b98c28eb3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #34 0x556b98c708fc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 SUMMARY: AddressSanitizer: heap-buffer-overflow /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim/src/../inst/include/hesim/stats/distributions.h:325:36 in hesim::stats::piecewise_exponential::piecewise_exponential(std::__1::vector>, std::__1::vector>) Shadow bytes around the buggy address: 0x7b8ecf82e280: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7b8ecf82e300: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7b8ecf82e380: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7b8ecf82e400: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7b8ecf82e480: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7b8ecf82e500: fa fa fa fa 00 00 00 00[fa]fa 00 00 00 00 fa fa 0x7b8ecf82e580: 00 00 00 00 fa fa fd fd fd fa fa fa 00 00 00 00 0x7b8ecf82e600: fa fa fd fd fd fa fa fa fd fd fd fa fa fa 00 00 0x7b8ecf82e680: 00 00 fa fa 00 00 00 00 fa fa fd fd fd fa fa fa 0x7b8ecf82e700: fd fd fd fa fa fa fd fd fd fa fa fa fd fd fd fa 0x7b8ecf82e780: fa fa fd fd fd fa fa fa fd fd fd fa fa fa fd fd Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user: f7 Container overflow: fc Array cookie: ac Intra object redzone: bb ASan internal: fe Left alloca redzone: ca Right alloca redzone: cb ==452793==ABORTING --- re-building ‘mlogit.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/mlogit_files/figure-html/stateprobs-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 31654 bytes Input file size = 31768 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27112 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27112 Output IDAT size = 27112 bytes (4542 bytes decrease) Output file size = 27190 bytes (4578 bytes = 14.41% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/mlogit_files/figure-html/icerHeterogeneity-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 23075 bytes Input file size = 23177 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18430 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18430 Output IDAT size = 18430 bytes (4645 bytes decrease) Output file size = 18508 bytes (4669 bytes = 20.14% decrease) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘mlogit.Rmd’ --- re-building ‘mstate.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/mstate_files/figure-html/predicted_hazards_plot-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 45465 bytes Input file size = 45603 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34672 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34672 Output IDAT size = 34672 bytes (10793 bytes decrease) Output file size = 34750 bytes (10853 bytes = 23.80% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/mstate_files/figure-html/stprobs_by_strategy_plot-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37293 bytes Input file size = 37419 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29249 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29249 Output IDAT size = 29249 bytes (8044 bytes decrease) Output file size = 29327 bytes (8092 bytes = 21.63% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/mstate_files/figure-html/stprobs_by_timescale_plot-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 33378 bytes Input file size = 33504 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26806 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26806 Output IDAT size = 26806 bytes (6572 bytes decrease) Output file size = 26884 bytes (6620 bytes = 19.76% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/mstate_files/figure-html/qalys_plot-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10114 bytes Input file size = 10204 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8807 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 8694 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 8694 Output IDAT size = 8694 bytes (1420 bytes decrease) Output file size = 8772 bytes (1432 bytes = 14.03% decrease) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘mstate.Rmd’ --- re-building ‘psm.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/psm_files/figure-html/survcurves-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 65503 bytes Input file size = 65665 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55645 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55645 Output IDAT size = 55645 bytes (9858 bytes decrease) Output file size = 55723 bytes (9942 bytes = 15.14% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/hesim.Rcheck/vign_test/hesim/vignettes/psm_files/figure-html/stateprobs-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 26478 bytes Input file size = 26592 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21446 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21446 Output IDAT size = 21446 bytes (5032 bytes decrease) Output file size = 21524 bytes (5068 bytes = 19.06% decrease) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘psm.Rmd’ SUMMARY: processing the following file failed: ‘markov-inhomogeneous-indiv.Rmd’ Error: Vignette re-building failed. Execution halted