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

--- re-building ‘model-description.Rmd’ using rmarkdown
--- finished re-building ‘model-description.Rmd’

--- re-building ‘nonlinear.Rmd’ using rmarkdown
=================================================================
==2210552==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7d6b94fc7570 at pc 0x7b9b7b0f4a16 bp 0x7ffebec83a70 sp 0x7ffebec83a68
READ of size 4 at 0x7d6b94fc7570 thread T0
    #0 0x7b9b7b0f4a15 in objective_function<double>::operator()() /data/gannet/ripley/R/packages/tests-clang-ASAN/dsem/src/dsem.cpp:453:13
    #1 0x7b9b7aae5b91 in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7
    #2 0x55ed9121af76 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763:11
    #3 0x55ed91228785 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11
    #4 0x55ed912d862a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14
    #5 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16
    #6 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8
    #7 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39
    #8 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16
    #9 0x55ed912cd26e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16
    #10 0x55ed912cabd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12
    #11 0x55ed91323a75 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8
    #12 0x55ed912ca6f0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12
    #13 0x55ed91328503 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13
    #14 0x55ed912d862a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14
    #15 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16
    #16 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8
    #17 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13
    #18 0x55ed912ca3a5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6
    #19 0x55ed91329733 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018:9
    #20 0x55ed913d2369 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11
    #21 0x55ed912dde43 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15
    #22 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16
    #23 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8
    #24 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13
    #25 0x55ed912ca3a5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6
    #26 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13
    #27 0x55ed912f7061 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5867:6
    #28 0x55ed912f7061 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7880:20
    #29 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16
    #30 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8
    #31 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39
    #32 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16
    #33 0x55ed912cd26e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16
    #34 0x55ed912cabd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12
    #35 0x55ed91328503 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13
    #36 0x55ed912d862a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14
    #37 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16
    #38 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8
    #39 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39
    #40 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16
    #41 0x55ed912cd26e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16
    #42 0x55ed912cabd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12
    #43 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39
    #44 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16
    #45 0x55ed912ebd6a in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16
    #46 0x55ed912ebd6a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16
    #47 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16
    #48 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8
    #49 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39
    #50 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16
    #51 0x55ed912cd26e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16
    #52 0x55ed912cabd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12
    #53 0x55ed9139ba91 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23
    #54 0x55ed9139e2c0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11
    #55 0x55ed9139e2c0 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5
    #56 0x55ed9139e352 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5
    #57 0x55ed9109fd3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5
    #58 0x7f9b98311574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1)
    #59 0x7f9b98311627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1)
    #60 0x55ed90fb77d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4)

0x7d6b94fc7570 is located 0 bytes after 2288-byte region [0x7d6b94fc6c80,0x7d6b94fc7570)
allocated by thread T0 here:
    #0 0x55ed9105cbb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3
    #1 0x7b9b7ad12fe6 in Eigen::internal::handmade_aligned_malloc(unsigned long, unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:105:20
    #2 0x7b9b7ad12fe6 in Eigen::internal::aligned_malloc(unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:188:14
    #3 0x7b9b7ad12fe6 in void* Eigen::internal::conditional_aligned_malloc<true>(unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:241:10
    #4 0x7b9b7ad12fe6 in int* Eigen::internal::conditional_aligned_new_auto<int, true>(unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:404:36
    #5 0x7b9b7ad12fe6 in Eigen::DenseStorage<int, -1, -1, 1, 0>::resize(long, long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/DenseStorage.h:639:20
    #6 0x7b9b7af7c899 in Eigen::PlainObjectBase<Eigen::Array<int, -1, 1, 0, -1, 1>>::resize(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285:19
    #7 0x7b9b7af7c899 in void Eigen::internal::resize_if_allowed<Eigen::Array<int, -1, 1, 0, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>, int, int>(Eigen::Array<int, -1, 1, 0, -1, 1>&, Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op<int, int> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:764:9
    #8 0x7b9b7af7c899 in void Eigen::internal::call_dense_assignment_loop<Eigen::Array<int, -1, 1, 0, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>, Eigen::internal::assign_op<int, int>>(Eigen::Array<int, -1, 1, 0, -1, 1>&, Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op<int, int> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:778:3
    #9 0x7b9b7af7c899 in Eigen::internal::Assignment<Eigen::Array<int, -1, 1, 0, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>, Eigen::internal::assign_op<int, int>, Eigen::internal::Dense2Dense, void>::run(Eigen::Array<int, -1, 1, 0, -1, 1>&, Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op<int, int> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5
    #10 0x7b9b7af7c899 in void Eigen::internal::call_assignment_no_alias<Eigen::Array<int, -1, 1, 0, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>, Eigen::internal::assign_op<int, int>>(Eigen::Array<int, -1, 1, 0, -1, 1>&, Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op<int, int> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3
    #11 0x7b9b7af7c899 in Eigen::Array<int, -1, 1, 0, -1, 1>& Eigen::PlainObjectBase<Eigen::Array<int, -1, 1, 0, -1, 1>>::_set_noalias<Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>>(Eigen::DenseBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797:7
    #12 0x7b9b7af7c899 in void Eigen::PlainObjectBase<Eigen::Array<int, -1, 1, 0, -1, 1>>::_init1<Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>>(Eigen::DenseBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:883:13
    #13 0x7b9b7af7c899 in Eigen::Array<int, -1, 1, 0, -1, 1>::Array<Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>>(Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Array.h:210:22
    #14 0x7b9b7af7c899 in tmbutils::vector<int>::vector<Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>>(Eigen::CwiseUnaryOp<Eigen::internal::scalar_cast_op<double, int>, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>> const>) /data/gannet/ripley/R/test-clang/TMB/include/tmbutils/vector.hpp:24:16
    #15 0x7b9b7af7c899 in tmbutils::vector<int> asVector<int>(SEXPREC*) /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:114:21
    #16 0x7b9b7b0c51e6 in objective_function<double>::operator()() /data/gannet/ripley/R/packages/tests-clang-ASAN/dsem/src/dsem.cpp:413:5
    #17 0x7b9b7aae5b91 in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7
    #18 0x55ed9121af76 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763:11
    #19 0x55ed91228785 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11
    #20 0x55ed912d862a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14
    #21 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16
    #22 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8
    #23 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39
    #24 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16
    #25 0x55ed912cd26e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16
    #26 0x55ed912cabd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12
    #27 0x55ed91323a75 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8
    #28 0x55ed912ca6f0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12
    #29 0x55ed91328503 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13
    #30 0x55ed912d862a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14
    #31 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16
    #32 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8
    #33 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13
    #34 0x55ed912ca3a5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6
    #35 0x55ed91329733 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018:9
    #36 0x55ed913d2369 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11
    #37 0x55ed912dde43 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15
    #38 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16
    #39 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8
    #40 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13
    #41 0x55ed912ca3a5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6
    #42 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13

SUMMARY: AddressSanitizer: heap-buffer-overflow /data/gannet/ripley/R/packages/tests-clang-ASAN/dsem/src/dsem.cpp:453:13 in objective_function<double>::operator()()
Shadow bytes around the buggy address:
  0x7d6b94fc7280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x7d6b94fc7300: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x7d6b94fc7380: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x7d6b94fc7400: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x7d6b94fc7480: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
=>0x7d6b94fc7500: 00 00 00 00 00 00 00 00 00 00 00 00 00 00[fa]fa
  0x7d6b94fc7580: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x7d6b94fc7600: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x7d6b94fc7680: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x7d6b94fc7700: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x7d6b94fc7780: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
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
==2210552==ABORTING
--- re-building ‘random_slopes.Rmd’ using rmarkdown
--- finished re-building ‘random_slopes.Rmd’

--- re-building ‘spatial_diffusion.Rmd’ using rmarkdown
Read 21 records
--- finished re-building ‘spatial_diffusion.Rmd’

SUMMARY: processing the following file failed:
  ‘nonlinear.Rmd’

Error: Vignette re-building failed.
Execution halted