R Under development (unstable) (2022-03-12 r81880) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > pkgname <- "FlywayNet" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('FlywayNet') > > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("estimate_migration_ABC") > ### * estimate_migration_ABC > > flush(stderr()); flush(stdout()) > > ### Name: estimate_migration_ABC > ### Title: Estimates migration parameters using an ABC method. > ### Aliases: estimate_migration_ABC > > ### ** Examples > > migr <- generate_toy_migration() > # Argument nb_simul just provide to reduce running time > estimated_migr <- estimate_migration_ABC( migr, nb_simul = 30 ) [1] " ------ Lenormand et al. (2012)'s algorithm ------" generate_trajectories_C.cpp:107:24: runtime error: nan is outside the range of representable values of type 'int' #0 0x7f8f537c0d0d in simulate_trajectories(Rcpp::Matrix<14, Rcpp::PreserveStorage>&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, int) /data/gannet/ripley/R/packages/tests-clang-SAN/FlywayNet/src/generate_trajectories_C.cpp:107:24 #1 0x7f8f537bde4a in generate_trajectories_C(Rcpp::Vector<19, Rcpp::PreserveStorage>, Rcpp::Nullable >, Rcpp::Nullable) /data/gannet/ripley/R/packages/tests-clang-SAN/FlywayNet/src/generate_trajectories_C.cpp:36:3 #2 0x7f8f5376fbd3 in _FlywayNet_generate_trajectories_C /data/gannet/ripley/R/packages/tests-clang-SAN/FlywayNet/src/RcppExports.cpp:65:34 #3 0x6e6f72 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:607:17 #4 0x7336f9 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1284:11 #5 0x8436f5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7136:14 #6 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #7 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #8 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #9 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #10 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #11 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #12 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #13 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #14 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #15 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #17 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #18 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #19 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #20 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #21 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #22 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #23 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #24 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #25 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #26 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #27 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #28 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #29 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #30 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #31 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #32 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #33 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #34 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #35 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #36 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #37 0x82ead8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:871:12 #38 0x8a29f1 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2991:8 #39 0x82e488 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:823:12 #40 0x95d8b6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #41 0x960e10 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:316:11 #42 0x960c19 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1137:5 #43 0x960f52 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1144:5 #44 0x4f30ba in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #45 0x7f8f62f78b74 in __libc_start_main (/lib64/libc.so.6+0x27b74) (BuildId: 08df60634339b221bb854d4e10b7278cafde70c4) #46 0x43231d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43231d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior generate_trajectories_C.cpp:107:24 in ================================================================= ==2042109==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x612000324aa0 at pc 0x7f8f537c1289 bp 0x7fffdbf31af0 sp 0x7fffdbf31ae8 READ of size 8 at 0x612000324aa0 thread T0 #0 0x7f8f537c1288 in simulate_trajectories(Rcpp::Matrix<14, Rcpp::PreserveStorage>&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, int) /data/gannet/ripley/R/packages/tests-clang-SAN/FlywayNet/src/generate_trajectories_C.cpp:119:22 #1 0x7f8f537bde4a in generate_trajectories_C(Rcpp::Vector<19, Rcpp::PreserveStorage>, Rcpp::Nullable >, Rcpp::Nullable) /data/gannet/ripley/R/packages/tests-clang-SAN/FlywayNet/src/generate_trajectories_C.cpp:36:3 #2 0x7f8f5376fbd3 in _FlywayNet_generate_trajectories_C /data/gannet/ripley/R/packages/tests-clang-SAN/FlywayNet/src/RcppExports.cpp:65:34 #3 0x6e6f72 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:607:17 #4 0x7336f9 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1284:11 #5 0x8436f5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7136:14 #6 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #7 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #8 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #9 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #10 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #11 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #12 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #13 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #14 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #15 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #17 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #18 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #19 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #20 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #21 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #22 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #23 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #24 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #25 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #26 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #27 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #28 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #29 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #30 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #31 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #32 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #33 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #34 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #35 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #36 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #37 0x82ead8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:871:12 #38 0x8a29f1 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2991:8 #39 0x82e488 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:823:12 #40 0x95d8b6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #41 0x960e10 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:316:11 #42 0x960c19 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1137:5 #43 0x960f52 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1144:5 #44 0x4f30ba in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #45 0x7f8f62f78b74 in __libc_start_main (/lib64/libc.so.6+0x27b74) (BuildId: 08df60634339b221bb854d4e10b7278cafde70c4) #46 0x43231d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43231d) 0x612000324aa0 is located 32 bytes to the left of 288-byte region [0x612000324ac0,0x612000324be0) allocated by thread T0 here: #0 0x4b57ae in malloc /data/gannet/ripley/Sources2/LLVM/14.0.0/llvm-project-14.0.0rc2.src/compiler-rt/lib/asan/asan_malloc_linux.cpp:69:3 #1 0x97bfe1 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2834:7 #2 0x7f8f537a5793 in Rcpp::Vector<14, Rcpp::PreserveStorage>::Vector(Rcpp::Dimension const&) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/vector/Vector.h:135:25 #3 0x7f8f537bf880 in Rcpp::Matrix<14, Rcpp::PreserveStorage>::Matrix(int const&, int const&) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/vector/Matrix.h:59:52 #4 0x7f8f537bf880 in simulate_trajectories(Rcpp::Matrix<14, Rcpp::PreserveStorage>&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, int) /data/gannet/ripley/R/packages/tests-clang-SAN/FlywayNet/src/generate_trajectories_C.cpp:82:23 #5 0x7f8f537bde4a in generate_trajectories_C(Rcpp::Vector<19, Rcpp::PreserveStorage>, Rcpp::Nullable >, Rcpp::Nullable) /data/gannet/ripley/R/packages/tests-clang-SAN/FlywayNet/src/generate_trajectories_C.cpp:36:3 #6 0x7f8f5376fbd3 in _FlywayNet_generate_trajectories_C /data/gannet/ripley/R/packages/tests-clang-SAN/FlywayNet/src/RcppExports.cpp:65:34 #7 0x6e6f72 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:607:17 #8 0x7336f9 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1284:11 #9 0x8436f5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7136:14 #10 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #11 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #12 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #13 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #14 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #15 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #17 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #18 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #19 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #20 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #21 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #22 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #23 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #24 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #25 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #26 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 #27 0x896934 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #28 0x8925bf in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1844:16 #29 0x85302f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7104:12 #30 0x82e09e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:748:8 SUMMARY: AddressSanitizer: heap-buffer-overflow /data/gannet/ripley/R/packages/tests-clang-SAN/FlywayNet/src/generate_trajectories_C.cpp:119:22 in simulate_trajectories(Rcpp::Matrix<14, Rcpp::PreserveStorage>&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, int) Shadow bytes around the buggy address: 0x0c248005c900: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c248005c910: 00 00 00 00 00 00 00 00 00 fa fa fa fa fa fa fa 0x0c248005c920: fa fa fa fa fa fa fa fa 00 00 00 00 00 00 00 00 0x0c248005c930: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c248005c940: 00 00 00 00 00 00 00 00 00 00 00 00 00 fa fa fa =>0x0c248005c950: fa fa fa fa[fa]fa fa fa 00 00 00 00 00 00 00 00 0x0c248005c960: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c248005c970: 00 00 00 00 00 00 00 00 00 00 00 00 fa fa fa fa 0x0c248005c980: fa fa fa fa fa fa fa fa 00 00 00 00 00 00 00 00 0x0c248005c990: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c248005c9a0: 00 00 00 00 00 00 00 00 00 00 00 00 fa fa fa fa 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 ==2042109==ABORTING