--- re-building ‘features.Rmd’ using rmarkdown Read 3 items Read 4 records --- finished re-building ‘features.Rmd’ --- re-building ‘model-description.Rmd’ using rmarkdown --- finished re-building ‘model-description.Rmd’ --- re-building ‘nonlinear.Rmd’ using rmarkdown ================================================================= ==1673532==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7d8b03b72570 at pc 0x7bbae1a8d55d bp 0x7ffcc42a70c0 sp 0x7ffcc42a70b8 READ of size 4 at 0x7d8b03b72570 thread T0 #0 0x7bbae1a8d55c in objective_function::operator()() /data/gannet/ripley/R/packages/tests-gcc-SAN/dsem/src/dsem.cpp:453 #1 0x7bbae19ea26d in getParameterOrder /data/gannet/ripley/R/test-dev/TMB/include/tmb_core.hpp:2065 #2 0x000000751446 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #3 0x000000755cca in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #4 0x0000008d7a62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #5 0x0000008c4cc3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #6 0x00000086374a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #7 0x00000087ba8a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #8 0x00000087fa3d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #9 0x000000863df8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #10 0x000000863df8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #11 0x00000089578e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #12 0x000000864226 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #13 0x00000089d301 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #14 0x0000008d7a62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #15 0x0000008c4cc3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #16 0x00000086374a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #17 0x000000931831 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #18 0x000000864dbc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #19 0x0000008a0223 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018 #20 0x000000a9f276 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424 #21 0x0000008e4c71 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #22 0x0000008c4cc3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #23 0x00000086374a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #24 0x000000931831 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #25 0x000000864dbc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #26 0x000000931831 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #27 0x0000008aa911 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #28 0x0000008aa911 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5867 #29 0x0000008e78dc in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7880 #30 0x0000008c4cc3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x00000086374a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x00000087ba8a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #33 0x00000087fa3d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #34 0x000000863df8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #35 0x000000863df8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #36 0x00000089d301 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #37 0x0000008d7a62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #38 0x0000008c4cc3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #39 0x00000086374a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #40 0x00000087ba8a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #41 0x00000087fa3d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #42 0x000000863df8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #43 0x000000863df8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #44 0x00000087ba8a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #45 0x00000087fa3d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #46 0x0000008810eb in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #47 0x0000008ec565 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #48 0x0000008c4cc3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #49 0x00000086374a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #50 0x00000087ba8a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #51 0x00000087fa3d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #52 0x000000863df8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #53 0x000000863df8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #54 0x000000a0c4c8 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #55 0x000000a0c4c8 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #56 0x000000a1b7ba in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #57 0x000000a1b852 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #58 0x00000041309f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #59 0x7fbb06e12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #60 0x7fbb06e12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #61 0x000000413a84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a84) (BuildId: 62f2656ce5bad6790bac4bcc2fb092357f4c8dca) 0x7d8b03b72570 is located 0 bytes after 2288-byte region [0x7d8b03b71c80,0x7d8b03b72570) allocated by thread T0 here: #0 0x7fbb086e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x7bbae186a574 in Eigen::internal::handmade_aligned_malloc(unsigned long, unsigned long) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/Memory.h:105 #2 0x7bbae186a574 in Eigen::internal::aligned_malloc(unsigned long) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/Memory.h:188 #3 0x7bbae1bc25c1 in void* Eigen::internal::conditional_aligned_malloc(unsigned long) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/Memory.h:241 #4 0x7bbae1bc25c1 in int* Eigen::internal::conditional_aligned_new_auto(unsigned long) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/Memory.h:404 #5 0x7bbae1bc25c1 in Eigen::DenseStorage::resize(long, long, long) [clone .constprop.0] /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/DenseStorage.h:639 #6 0x7bbae1af8783 in Eigen::PlainObjectBase >::resize(long, long) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285 #7 0x7bbae1af8783 in void Eigen::internal::resize_if_allowed, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const>, int, int>(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:764 #8 0x7bbae1af8783 in void Eigen::internal::call_dense_assignment_loop, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const>, Eigen::internal::assign_op >(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:778 #9 0x7bbae1af8783 in Eigen::internal::Assignment, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #10 0x7bbae1af8783 in void Eigen::internal::call_assignment_no_alias, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const>, Eigen::internal::assign_op >(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #11 0x7bbae1af8783 in Eigen::Array& Eigen::PlainObjectBase >::_set_noalias, Eigen::Map, 0, Eigen::Stride<0, 0> > const> >(Eigen::DenseBase, Eigen::Map, 0, Eigen::Stride<0, 0> > const> > const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797 #12 0x7bbae1af8783 in void Eigen::PlainObjectBase >::_init1, Eigen::Map, 0, Eigen::Stride<0, 0> > const>, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const> >(Eigen::DenseBase, Eigen::Map, 0, Eigen::Stride<0, 0> > const> > const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:883 #13 0x7bbae1af8783 in Eigen::Array::Array, Eigen::Map, 0, Eigen::Stride<0, 0> > const> >(Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const> const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Array.h:210 #14 0x7bbae1af8783 in tmbutils::vector::vector, Eigen::Map, 0, Eigen::Stride<0, 0> > const> >(Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0> > const>) /data/gannet/ripley/R/test-dev/TMB/include/tmbutils/vector.hpp:24 #15 0x7bbae1af8783 in tmbutils::vector asVector(SEXPREC*) /data/gannet/ripley/R/test-dev/TMB/include/convert.hpp:114 #16 0x7bbae1a833f3 in objective_function::operator()() /data/gannet/ripley/R/packages/tests-gcc-SAN/dsem/src/dsem.cpp:413 #17 0x7bbae19ea26d in getParameterOrder /data/gannet/ripley/R/test-dev/TMB/include/tmb_core.hpp:2065 #18 0x000000751446 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #19 0x000000755cca in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #20 0x0000008d7a62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #21 0x0000008c4cc3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #22 0x00000086374a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000087ba8a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #24 0x00000087fa3d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #25 0x000000863df8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #26 0x000000863df8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #27 0x00000089578e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #28 0x000000864226 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #29 0x00000089d301 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #30 0x0000008d7a62 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #31 0x0000008c4cc3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #32 0x00000086374a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #33 0x000000931831 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #34 0x000000864dbc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #35 0x0000008a0223 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018 #36 0x000000a9f276 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424 #37 0x0000008e4c71 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #38 0x0000008c4cc3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #39 0x00000086374a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #40 0x000000931831 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #41 0x000000864dbc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #42 0x000000931831 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 SUMMARY: AddressSanitizer: heap-buffer-overflow /data/gannet/ripley/R/packages/tests-gcc-SAN/dsem/src/dsem.cpp:453 in objective_function::operator()() Shadow bytes around the buggy address: 0x7d8b03b72280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d8b03b72300: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d8b03b72380: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d8b03b72400: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d8b03b72480: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x7d8b03b72500: 00 00 00 00 00 00 00 00 00 00 00 00 00 00[fa]fa 0x7d8b03b72580: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d8b03b72600: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d8b03b72680: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d8b03b72700: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d8b03b72780: 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 ==1673532==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