--- re-building ‘cea.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/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-gcc-SAN/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-gcc-SAN/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-gcc-SAN/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-gcc-SAN/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-gcc-SAN/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-gcc-SAN/hesim.Rcheck/vign_test/hesim/vignettes/intro_files/figure-html/ceac_plot-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24750 bytes Input file size = 24864 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19241 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 = 19241 Output IDAT size = 19241 bytes (5509 bytes decrease) Output file size = 19319 bytes (5545 bytes = 22.30% 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-gcc-SAN/hesim.Rcheck/vign_test/hesim/vignettes/markov-cohort_files/figure-html/simStateprobsPlot-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 76503 bytes Input file size = 76689 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63017 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 = 63017 Output IDAT size = 63017 bytes (13486 bytes decrease) Output file size = 63095 bytes (13594 bytes = 17.73% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/hesim.Rcheck/vign_test/hesim/vignettes/markov-cohort_files/figure-html/ceac-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 23516 bytes Input file size = 23618 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18988 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 = 18988 Output IDAT size = 18988 bytes (4528 bytes decrease) Output file size = 19066 bytes (4552 bytes = 19.27% 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-gcc-SAN/hesim.Rcheck/vign_test/hesim/vignettes/markov-inhomogeneous-cohort_files/figure-html/simStateprobsPlot-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 46683 bytes Input file size = 46821 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36501 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 = 36501 Output IDAT size = 36501 bytes (10182 bytes decrease) Output file size = 36579 bytes (10242 bytes = 21.87% decrease) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘markov-inhomogeneous-cohort.Rmd’ --- re-building ‘markov-inhomogeneous-indiv.Rmd’ using rmarkdown ================================================================= ==4102410==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7bac1bc367f0 at pc 0x7b7c05ef6bc1 bp 0x7ffe9463b9c0 sp 0x7ffe9463b9b8 READ of size 8 at 0x7bac1bc367f0 thread T0 #0 0x7b7c05ef6bc0 in hesim::stats::piecewise_exponential::piecewise_exponential(std::vector >, std::vector >) ../inst/include/hesim/stats/distributions.h:325 #1 0x7b7c05f92e61 in hesim::statmods::surv::init_dist_(hesim::statmods::params_surv) ../inst/include/hesim/statmods/statmods.h:174 #2 0x7b7c05f92e61 in hesim::statmods::surv::surv(std::vector, std::allocator > >, hesim::statmods::params_surv) ../inst/include/hesim/statmods/statmods.h:223 #3 0x7b7c05f96f98 in hesim::ctstm::mstate_list::init_survmods_(Rcpp::Environment_Impl) ../inst/include/hesim/ctstm/ctstm.h:187 #4 0x7b7c05fb1a1f in hesim::ctstm::mstate_list::mstate_list(Rcpp::Environment_Impl) ../inst/include/hesim/ctstm/ctstm.h:200 #5 0x7b7c05fb1a1f in hesim::ctstm::transmod::create(Rcpp::Environment_Impl) ../inst/include/hesim/ctstm/ctstm.h:238 #6 0x7b7c0643d8f4 in C_ctstm_sim_disease(Rcpp::Environment_Impl, std::vector >, std::vector >, std::vector >, int, std::__cxx11::basic_string, std::allocator >, std::vector >, std::vector >, double, double, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/hesim/src/indiv-ctstm.cpp:33 #7 0x7b7c05e914a2 in _hesim_C_ctstm_sim_disease /data/gannet/ripley/R/packages/tests-gcc-SAN/hesim/src/RcppExports.cpp:206 #8 0x00000074becf in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:801 #9 0x000000750eaa in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #10 0x0000008cca32 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #11 0x0000008b9c7b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #12 0x000000859ff2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x00000086fd3a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #14 0x000000873dfa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #15 0x00000085a693 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #16 0x00000085a693 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #17 0x000000888a8e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #18 0x00000085aab6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #19 0x00000086e53b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992 #20 0x00000085aab6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #21 0x00000086fd3a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #22 0x000000873dfa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #23 0x00000085a693 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #24 0x00000085a693 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #25 0x000000880c38 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3384 #26 0x00000085aab6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #27 0x00000086e53b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992 #28 0x00000085aab6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #29 0x00000086fd3a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #30 0x000000873dfa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #31 0x00000085a693 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #32 0x00000085a693 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #33 0x000000890031 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #34 0x0000008cca32 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #35 0x0000008b9c7b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #36 0x000000859ff2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #37 0x000000921311 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #38 0x00000085b64c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #39 0x000000892af3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980 #40 0x000000a91bf6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #41 0x0000008d9c41 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #42 0x0000008b9c7b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #43 0x000000859ff2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #44 0x000000921311 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #45 0x00000085b64c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #46 0x000000921311 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #47 0x0000008a4b51 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #48 0x0000008a4b51 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831 #49 0x0000008dc8ac in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844 #50 0x0000008b9c7b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #51 0x000000859ff2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x00000086fd3a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #53 0x000000873dfa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #54 0x00000085a693 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #55 0x00000085a693 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #56 0x000000890031 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #57 0x0000008cca32 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #58 0x0000008b9c7b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #59 0x000000859ff2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #60 0x00000086fd3a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #61 0x000000873dfa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #62 0x00000085a693 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #63 0x00000085a693 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #64 0x00000086fd3a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #65 0x000000873dfa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #66 0x0000008e1535 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #67 0x0000008e1535 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #68 0x0000008b9c7b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #69 0x000000859ff2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #70 0x00000086fd3a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #71 0x000000873dfa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #72 0x00000085a693 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #73 0x00000085a693 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #74 0x000000a001c8 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #75 0x000000a001c8 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #76 0x000000a055fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #77 0x000000a0f812 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #78 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #79 0x7f7c1f2115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #80 0x7f7c1f2116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #81 0x000000413b84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b84) (BuildId: 3c6421a284bb14a2d72a60ac77326376d6083d38) 0x7bac1bc367f0 is located 0 bytes after 32-byte region [0x7bac1bc367d0,0x7bac1bc367f0) allocated by thread T0 here: #0 0x7f7c20ae7a1b in operator new(unsigned long) (/lib64/libasan.so.8+0xe7a1b) (BuildId: 7f1aa7e2e600e8c9d54ce6e3d36f3d31bfe7949a) #1 0x7b7c05fac02d in std::__new_allocator::allocate(unsigned long, void const*) /usr/include/c++/15/bits/new_allocator.h:151 #2 0x7b7c05fac02d in std::allocator_traits >::allocate(std::allocator&, unsigned long) /usr/include/c++/15/bits/alloc_traits.h:614 #3 0x7b7c05fac02d in std::_Vector_base >::_M_allocate(unsigned long) /usr/include/c++/15/bits/stl_vector.h:387 #4 0x7b7c05fac02d in std::_Vector_base >::_M_allocate(unsigned long) /usr/include/c++/15/bits/stl_vector.h:384 #5 0x7b7c05fac02d in double* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned long, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) /usr/include/c++/15/bits/stl_vector.h:1910 #6 0x7b7c05fac02d in std::vector >::operator=(std::vector > const&) /usr/include/c++/15/bits/vector.tcc:238 #7 0x7b7c05ef5d00 in hesim::stats::piecewise_exponential::piecewise_exponential(std::vector >, std::vector >) ../inst/include/hesim/stats/distributions.h:321 #8 0x7b7c05f92e61 in hesim::statmods::surv::init_dist_(hesim::statmods::params_surv) ../inst/include/hesim/statmods/statmods.h:174 #9 0x7b7c05f92e61 in hesim::statmods::surv::surv(std::vector, std::allocator > >, hesim::statmods::params_surv) ../inst/include/hesim/statmods/statmods.h:223 #10 0x7b7c05f96f98 in hesim::ctstm::mstate_list::init_survmods_(Rcpp::Environment_Impl) ../inst/include/hesim/ctstm/ctstm.h:187 #11 0x7b7c05fb1a1f in hesim::ctstm::mstate_list::mstate_list(Rcpp::Environment_Impl) ../inst/include/hesim/ctstm/ctstm.h:200 #12 0x7b7c05fb1a1f in hesim::ctstm::transmod::create(Rcpp::Environment_Impl) ../inst/include/hesim/ctstm/ctstm.h:238 #13 0x7b7c0643d8f4 in C_ctstm_sim_disease(Rcpp::Environment_Impl, std::vector >, std::vector >, std::vector >, int, std::__cxx11::basic_string, std::allocator >, std::vector >, std::vector >, double, double, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/hesim/src/indiv-ctstm.cpp:33 #14 0x7b7c05e914a2 in _hesim_C_ctstm_sim_disease /data/gannet/ripley/R/packages/tests-gcc-SAN/hesim/src/RcppExports.cpp:206 #15 0x00000074becf in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:801 #16 0x000000750eaa in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #17 0x0000008cca32 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #18 0x0000008b9c7b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #19 0x000000859ff2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #20 0x00000086fd3a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #21 0x000000873dfa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #22 0x00000085a693 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #23 0x00000085a693 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #24 0x000000888a8e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #25 0x00000085aab6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #26 0x00000086e53b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992 #27 0x00000085aab6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #28 0x00000086fd3a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #29 0x000000873dfa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #30 0x00000085a693 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #31 0x00000085a693 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #32 0x000000880c38 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3384 #33 0x00000085aab6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #34 0x00000086e53b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992 #35 0x00000085aab6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #36 0x00000086fd3a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #37 0x000000873dfa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #38 0x00000085a693 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #39 0x00000085a693 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 SUMMARY: AddressSanitizer: heap-buffer-overflow ../inst/include/hesim/stats/distributions.h:325 in hesim::stats::piecewise_exponential::piecewise_exponential(std::vector >, std::vector >) Shadow bytes around the buggy address: 0x7bac1bc36500: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7bac1bc36580: fa fa fa fa fa fa fa fa 00 00 00 00 fa fa fa fa 0x7bac1bc36600: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7bac1bc36680: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7bac1bc36700: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7bac1bc36780: fa fa fa fa fa fa fa fa fa fa 00 00 00 00[fa]fa 0x7bac1bc36800: fd fd fd fa fa fa 00 00 00 00 fa fa 00 00 00 00 0x7bac1bc36880: fa fa fd fd fd fa fa fa 00 00 00 00 fa fa 00 00 0x7bac1bc36900: 00 00 fa fa fd fd fd fa fa fa fd fd fd fa fa fa 0x7bac1bc36980: fd fd fd fa fa fa fd fd fd fa fa fa fd fd fd fa 0x7bac1bc36a00: 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 ==4102410==ABORTING --- re-building ‘mlogit.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/hesim.Rcheck/vign_test/hesim/vignettes/mlogit_files/figure-html/stateprobs-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 31229 bytes Input file size = 31343 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26769 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 = 26769 Output IDAT size = 26769 bytes (4460 bytes decrease) Output file size = 26847 bytes (4496 bytes = 14.34% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/hesim.Rcheck/vign_test/hesim/vignettes/mlogit_files/figure-html/icerHeterogeneity-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27165 bytes Input file size = 27279 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21372 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 = 21372 Output IDAT size = 21372 bytes (5793 bytes decrease) Output file size = 21450 bytes (5829 bytes = 21.37% 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-gcc-SAN/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-gcc-SAN/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 = 37324 bytes Input file size = 37450 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29260 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 = 29260 Output IDAT size = 29260 bytes (8064 bytes decrease) Output file size = 29338 bytes (8112 bytes = 21.66% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/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 = 33511 bytes Input file size = 33637 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26819 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 = 26819 Output IDAT size = 26819 bytes (6692 bytes decrease) Output file size = 26897 bytes (6740 bytes = 20.04% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/hesim.Rcheck/vign_test/hesim/vignettes/mstate_files/figure-html/qalys_plot-1.png 576x384 pixels, 8 bits/pixel, 256 colors in palette Input IDAT size = 5434 bytes Input file size = 6292 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4021 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 = 4021 Output IDAT size = 4021 bytes (1413 bytes decrease) Output file size = 4879 bytes (1413 bytes = 22.46% 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-gcc-SAN/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-gcc-SAN/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