* using log directory ‘/data/gannet/ripley/R/packages/tests-clang-ASAN/lme4.Rcheck’ * using R Under development (unstable) (2026-07-04 r90207) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 22.1.8 (https://github.com/llvm/llvm-project ca7933e47d3a3451d81e72ac174dcb5aa28b59d1) flang version 22.1.8 (https://github.com/llvm/llvm-project ca7933e47d3a3451d81e72ac174dcb5aa28b59d1) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-07-05 14:24:44 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘lme4/DESCRIPTION’ ... OK * this is package ‘lme4’ version ‘2.0-1’ * package encoding: UTF-8 * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package ‘lme4’ can be installed ... [254s/329s] OK * used C++ compiler: ‘clang version 22.1.8 (https://github.com/llvm/llvm-project ca7933e47d3a3451d81e72ac174dcb5aa28b59d1)’ * checking package directory ... OK * checking whether the package can be loaded ... [13s/20s] OK * checking whether the package can be loaded with stated dependencies ... [13s/23s] OK * checking whether the package can be unloaded cleanly ... [13s/18s] OK * checking whether the namespace can be loaded with stated dependencies ... [11s/18s] OK * checking whether the namespace can be unloaded cleanly ... [14s/22s] OK * checking loading without being on the library search path ... [13s/21s] OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [28s/47s] ERROR Running examples in ‘lme4-Ex.R’ failed The error most likely occurred in: > ### Name: cbpp > ### Title: Contagious bovine pleuropneumonia > ### Aliases: cbpp cbpp2 > ### Keywords: datasets > > ### ** Examples > > ## response as a matrix > (m1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), + family = binomial, data = cbpp)) ================================================================= ==460053==ERROR: AddressSanitizer: heap-use-after-free on address 0x7d7215c408b0 at pc 0x7bb201c3b93c bp 0x7ffce750a7d0 sp 0x7ffce750a7c8 READ of size 16 at 0x7d7215c408b0 thread T0 #0 0x7bb201c3b93b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7bb201c3b93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7bb201c3b93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7bb201c3b93b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7bb201c3b93b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7bb201c3b93b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7bb201c3b93b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7bb201c3b93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7bb201c3b93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7bb201c3b93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7bb201c3b93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7bb201c3b93b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7bb201bc9cd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7bb201bc9cd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7bb201bc8bc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x563b03640b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x563b03704d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x563b036eb301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x563b036ee3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x563b036ebd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x563b03744bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x563b036eb840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x563b03742269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x563b036eb840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x563b0370ceba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x563b0370ceba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x563b036eb301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x563b036ed60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x563b036eb4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x563b036ed9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x563b036eb9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x563b03744bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x563b036eb840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x563b036ed9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x563b036eb9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x563b036ed9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x563b036eb9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x563b036ed60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x563b036eb2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x563b036f977a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x563b036eb301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x563b036ee3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x563b036ebd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x563b03742269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x563b036eb840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x563b0370ceba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x563b0370ceba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x563b036eb301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x563b036ee3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x563b036ebd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x563b035a1abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x563b036f977a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x563b036eb301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x563b036ee3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x563b036ebd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x563b03744bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x563b036eb840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x563b036ed9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #75 0x563b036eb9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #76 0x563b037bcbe1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #77 0x563b037bf410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #78 0x563b037bf410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #79 0x563b037bf4a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #80 0x563b034c0d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #81 0x7fb219212574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #82 0x7fb219212627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x563b033d87d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7d7215c408b0 is located 48 bytes inside of 1840-byte region [0x7d7215c40880,0x7d7215c40fb0) freed by thread T0 here: #0 0x563b0347d916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x563b037da31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x563b037da31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x563b037cd18b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x563b037e35c9 in Rf_NewEnvironment /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2571:2 #5 0x563b0373d04f in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2499:22 #6 0x7fb219070f40 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154:19 #7 0x563b03802853 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348:13 #8 0x563b03707a1f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085:12 #9 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #10 0x563b036eb301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #11 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #12 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #13 0x563b036ee3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #14 0x563b03803e97 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687:10 #15 0x563b0372ba0f in tryDispatch /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6090:16 #16 0x563b036f91c2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8320:19 #17 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x563b036eb301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x563b036ee3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x563b036ebd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x563b03744bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x563b036eb840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x563b03742269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x563b036eb840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x563b0370ceba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x563b0370ceba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 previously allocated by thread T0 here: #0 0x563b0347dbb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x563b037c7c7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x563b0352032b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x563b0352032b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7bb20c8420ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x563b03635365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x563b036f977a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x563b036eb301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x563b036ee3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x563b037f9e14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x563b037f8a98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x563b037fb073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x563b036fef93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x563b036eb301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x563b036ee3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x563b036ebd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x563b03749653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x563b036f977a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x563b036ecd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x563b036eb301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x563b03733a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x563b03732c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x563b036ee3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x563b036ebd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x563b03744bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7d7215c40600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7215c40680: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7215c40700: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7215c40780: fd fd fd fd fd fd fa fa fa fa fa fa fa fa fa fa 0x7d7215c40800: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d7215c40880: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7d7215c40900: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7215c40980: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7215c40a00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7215c40a80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7215c40b00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==460053==ABORTING * checking tests ... [19m/29m] ERROR Running ‘AAAtest-all.R’ [29s/52s] Running ‘HSAURtrees.R’ [15s/25s] Running ‘REMLdev.R’ [15s/24s] Running ‘ST.R’ [14s/19s] Running ‘agridat_gotway.R’ [14s/21s] Running ‘bootMer.R’ [41s/104s] Running ‘boundary.R’ [101s/176s] Running ‘confint.R’ [27s/40s] Running ‘devCritFun.R’ [14s/22s] Running ‘drop.R’ [18s/29s] Running ‘drop1contrasts.R’ [17s/25s] Running ‘dynload.R’ [39s/51s] Running ‘elston.R’ [15s/23s] Running ‘evalCall.R’ [15s/22s] Running ‘extras.R’ [13s/17s] Running ‘falsezero_dorie.R’ [13s/18s] Running ‘fewlevels.R’ Running ‘getME.R’ [19s/31s] Running ‘glmer-1.R’ [17s/33s] Running ‘glmerControlPass.R’ [22s/32s] Running ‘glmerWarn.R’ [23s/33s] Running ‘glmmExt.R’ [32s/47s] Running ‘glmmWeights.R’ [21s/30s] Running ‘hatvalues.R’ [14s/17s] Running ‘is.R’ [17s/25s] Running ‘lmList-tst.R’ [16s/20s] Running ‘lme4_nlme.R’ [16s/22s] Running ‘lmer-0.R’ [17s/25s] Running ‘lmer-1.R’ [13s/20s] Running ‘lmer-conv.R’ [14s/19s] Running ‘lmer2_ex.R’ [13s/18s] Running ‘methods.R’ [22s/31s] Running ‘minval.R’ [16s/27s] Running ‘modFormula.R’ [25s/37s] Running ‘nbinom.R’ [13s/16s] Running ‘nlmer-conv.R’ [13s/18s] Running ‘nlmer.R’ [16s/21s] Running ‘offset.R’ [19s/27s] Running ‘optimizer.R’ [21s/27s] Running ‘polytomous.R’ [14s/20s] Running ‘prLogistic.R’ [13s/19s] Running ‘predict_basis.R’ [19s/26s] Running ‘predsim.R’ [21s/33s] Running ‘priorWeights.R’ [34s/46s] Running ‘priorWeightsModComp.R’ [24s/35s] Running ‘profile-tst.R’ [14s/22s] Running ‘refit.R’ [14s/19s] Running ‘resids.R’ [16s/25s] Running ‘respiratory.R’ [17s/23s] Running ‘simulate.R’ [15s/23s] Running ‘test-glmernbref.R’ [22s/31s] Running ‘testOptControl.R’ [15s/22s] Running ‘testcolonizer.R’ [18s/29s] Running ‘testcrab.R’ [17s/28s] Running ‘throw.R’ [19s/27s] Running ‘varcorr.R’ [16s/26s] Running ‘vcov-etc.R’ [14s/21s] Running the tests in ‘tests/AAAtest-all.R’ failed. Complete output: > if (base::require("testthat", quietly = TRUE)) { + pkg <- "lme4" + require(pkg, character.only=TRUE, quietly=TRUE) + if(getRversion() < "3.5.0") { withAutoprint <- identity ; prt <- print } else { prt <- identity } + if(Sys.getenv("USER") %in% c("maechler", "bbolker")) withAutoprint({ + ## for developers' sake: + lP <- .libPaths() # ---- .libPaths() : ---- + prt(lP) + ## ---- Entries in .libPaths()[1] : ---- + prt(list.files(lP[1], include.dirs=TRUE)) + prt(sessionInfo()) + prt(packageDescription("Matrix")) + ## 'lme4' from packageDescription "file" : + prt(attr(packageDescription("lme4"), "file")) + }) + test_check(pkg) + ##======== ^^^ + print(warnings()) # TODO? catch most of these by expect_warning(..) + } else { + cat( "package 'testthat' not available, cannot run unit tests\n" ) + } ================================================================= ==464039==ERROR: AddressSanitizer: heap-use-after-free on address 0x7ce75eac50b0 at pc 0x7b274a80093c bp 0x7ffdb1945b10 sp 0x7ffdb1945b08 READ of size 16 at 0x7ce75eac50b0 thread T0 #0 0x7b274a80093b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7b274a80093b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7b274a80093b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7b274a80093b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7b274a80093b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7b274a80093b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7b274a80093b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7b274a80093b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7b274a80093b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7b274a80093b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7b274a80093b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7b274a80093b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7b274a78ecd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7b274a78ecd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7b274a78dbc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x562a5e4aeb06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x562a5e572d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x562a5e559d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x562a5e5b2bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x562a5e559840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x562a5e5b0269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x562a5e559840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x562a5e57aeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x562a5e57aeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #34 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #35 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #36 0x562a5e559d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #37 0x562a5e5b2bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x562a5e559840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x562a5e4a3365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #40 0x562a5e56777a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #41 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #42 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #43 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #44 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #45 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #46 0x562a5e559d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #47 0x562a5e5b0269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #48 0x562a5e559840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #49 0x562a5e5b7653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #50 0x562a5e56777a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #51 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #52 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #53 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #54 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #55 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #56 0x562a5e559d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #57 0x562a5e5b7fba in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993:9 #58 0x562a5e56777a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #59 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #60 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #61 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #62 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #63 0x562a5e5aa744 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #64 0x562a5e5aa744 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2465:8 #65 0x562a5e361d11 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75:8 #66 0x562a5e6614b9 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11 #67 0x562a5e56cf93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #68 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #69 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #70 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #71 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #72 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #73 0x562a5e559d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #74 0x562a5e5b0269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #75 0x562a5e559840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #76 0x562a5e559840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #77 0x562a5e62abe1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #78 0x562a5e62d410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #79 0x562a5e62d410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #80 0x562a5e62d4a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #81 0x562a5e32ed3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #82 0x7f2762012574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x7f2762012627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #84 0x562a5e2467d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7ce75eac50b0 is located 48 bytes inside of 1840-byte region [0x7ce75eac5080,0x7ce75eac57b0) freed by thread T0 here: #0 0x562a5e2eb916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x562a5e64831b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x562a5e64831b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x562a5e63b18b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x562a5e650fc5 in CONS_NR /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2519:2 #5 0x562a5e56bcfa in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8059:21 #6 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #7 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #8 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #9 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #10 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #11 0x562a5e559d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #12 0x562a5e53ebe4 in evalKeepVis /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:43:16 #13 0x562a5e53ebe4 in vsignalWarning /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:1808:2 #14 0x562a5e53e388 in Rf_warningcall /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:562:5 #15 0x562a5e5476e9 in do_warning /data/gannet/ripley/R/svn/R-devel/src/main/errors.c #16 0x562a5e56777a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #17 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x562a5e559d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x562a5e5b2bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x562a5e559840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x562a5e4a3365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #26 0x562a5e56777a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #27 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #28 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #29 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #30 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #31 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 previously allocated by thread T0 here: #0 0x562a5e2ebbb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x562a5e635c7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x562a5e38e32b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x562a5e38e32b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7b27514d80ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x562a5e4a3365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x562a5e56777a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x562a5e667e14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x562a5e666a98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x562a5e669073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x562a5e56cf93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x562a5e559d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x562a5e5b7653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x562a5e56777a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x562a5e55ad74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x562a5e559301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x562a5e5a1a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x562a5e5a0c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x562a5e55c3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x562a5e559d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x562a5e5b2bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7ce75eac4e00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ce75eac4e80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ce75eac4f00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ce75eac4f80: fd fd fd fd fd fd fa fa fa fa fa fa fa fa fa fa 0x7ce75eac5000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7ce75eac5080: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7ce75eac5100: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ce75eac5180: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ce75eac5200: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ce75eac5280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ce75eac5300: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==464039==ABORTING Running the tests in ‘tests/agridat_gotway.R’ failed. Complete output: > ## require(agridat) > ## dat <- gotway.hessianfly > > if (.Platform$OS.type != "windows") { + ## don't actually use gotway_hessianfly_fit or gotway_hessianfly_prof, + ## so we should be OK even with R< 3.0.1 + load(system.file("testdata","gotway_hessianfly.rda",package="lme4")) + # Block random. See Glimmix manual, output 1.18. + # Note: (Different parameterization) + + ## require("lme4.0") + ## fit2 <- glmer(cbind(y, n-y) ~ gen + (1|block), data=dat, family=binomial) + ## params <- list(fixef=fixef(fit2),theta=getME(fit2,"theta")) + ## detach("package:lme4.0") + lme4.0fit <- structure(list(fixef = structure(c(1.50345713031203, -0.193853259383803, + -0.540808391060274, -1.43419379979154, -0.203701042949808, -0.978322555343941, + -0.604078624475678, -1.67742449813309, -1.39842466673692, -0.681709344788684, + -1.46295367186169, -1.45908310198959, -3.55285756517073, -2.50731975980307, + -2.08716296677356, -2.96974270029992), .Names = c("(Intercept)", + "genG02", "genG03", "genG04", "genG05", "genG06", "genG07", "genG08", + "genG09", "genG10", "genG11", "genG12", "genG13", "genG14", "genG15", + "genG16")), theta = structure(0.0319087494293615, .Names = "block.(Intercept)")), .Names = c("fixef", + "theta")) + + ## start doesn't work because we don't get there + library(lme4) + m1 <- glmer(cbind(y, n-y) ~ gen + (1|block), data=gotway.hessianfly, + family=binomial) + m1B <- update(m1,control=glmerControl(optimizer="bobyqa")) + max(abs(m1@optinfo$derivs$gradient)) ## 0.0012 + max(abs(m1B@optinfo$derivs$gradient)) ## 2.03e-5 + abs(m1@optinfo$derivs$gradient)/abs(m1B@optinfo$derivs$gradient) + ## bobyqa gets gradients *at least* 1.64* lower + + lme4fit <- list(fixef=fixef(m1),theta=getME(m1,"theta")) + + ## hack around slight naming differences + lme4fit$theta <- unname(lme4fit$theta) + lme4.0fit$theta <- unname(lme4.0fit$theta) + ## difference in theta on x86_64-w64-mingw32 (64-bit) with r-devel is 0.000469576 + stopifnot(all.equal(lme4fit, lme4.0fit, tolerance = 5e-4)) + + ## Fun stuff: visualize and alternative model + + ## library(ggplot2) + ## dat$prop <- dat$y/dat$n + ## theme_set(theme_bw()) + ## ggplot(dat,aes(x=gen,y=prop,colour=block))+geom_point(aes(size=n))+ + ## geom_line(aes(group=block,colour=block))+ + ## geom_smooth(family=binomial,aes(weight=n,colour=block,group=block),method="glm", + ## alpha=0.1) + + ## dat$obs <- factor(seq(nrow(dat))) + ## m2 <- glmer(cbind(y, n-y) ~ block+ (1|gen) + (1|obs), data=dat, family=binomial) + + } ## not on windows/CRAN Loading required package: Matrix ================================================================= ==474479==ERROR: AddressSanitizer: heap-use-after-free on address 0x7daeae2c0930 at pc 0x7b5e8c8ce93c bp 0x7ffc2a6842b0 sp 0x7ffc2a6842a8 READ of size 16 at 0x7daeae2c0930 thread T0 #0 0x7b5e8c8ce93b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7b5e8c8ce93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7b5e8c8ce93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7b5e8c8ce93b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7b5e8c8ce93b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7b5e8c8ce93b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7b5e8c8ce93b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7b5e8c8ce93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7b5e8c8ce93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7b5e8c8ce93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7b5e8c8ce93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7b5e8c8ce93b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7b5e8c85ccd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7b5e8c85ccd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7b5e8c85bbc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x564b89f71b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x564b8a035d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x564b8a01dd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x564b8a01c301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x564b8a063c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x564b8a01f3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x564b8a01cd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x564b8a075bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x564b8a01c840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x564b8a073269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x564b8a01c840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x564b8a063c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x564b8a03deba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x564b8a03deba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x564b8a01dd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x564b8a01c301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x564b8a01e60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x564b8a01c4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x564b8a01e9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x564b8a01c9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x564b8a075bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x564b8a01c840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x564b8a01e9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x564b8a01c9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x564b8a01e9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x564b8a01c9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x564b8a01e60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x564b8a01c2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x564b8a02a77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x564b8a01dd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x564b8a01c301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x564b8a063c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x564b8a01f3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x564b8a01cd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x564b8a073269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x564b8a01c840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x564b8a063c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x564b8a03deba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x564b8a03deba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x564b8a01dd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x564b8a01c301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x564b8a063c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x564b8a01f3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x564b8a01cd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x564b89ed2abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x564b8a02a77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x564b8a01dd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x564b8a01c301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x564b8a063c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x564b8a01f3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x564b8a01cd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x564b8a075bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x564b8a01c840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x564b8a073269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #75 0x564b8a01c840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #76 0x564b8a01c840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #77 0x564b8a0edbe1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #78 0x564b8a0f0410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #79 0x564b8a0f0410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #80 0x564b8a0f04a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #81 0x564b89df1d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #82 0x7f5ea3f11574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x7f5ea3f11627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #84 0x564b89d097d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7daeae2c0930 is located 48 bytes inside of 8240-byte region [0x7daeae2c0900,0x7daeae2c2930) freed by thread T0 here: #0 0x564b89dae916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x564b8a10b31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x564b8a10b31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x564b8a0fe18b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x564b8a113fc5 in CONS_NR /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2519:2 #5 0x564b8a0f522a in Rf_matchArgs_NR /data/gannet/ripley/R/svn/R-devel/src/main/match.c:196:12 #6 0x564b8a0f6c58 in Rf_matchArgs_RC /data/gannet/ripley/R/svn/R-devel/src/main/match.c:392:17 #7 0x564b8a063fa6 in make_applyClosure_env /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2261:15 #8 0x564b8a063b25 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2304:19 #9 0x564b8a01f3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #10 0x564b8a01cd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #11 0x564b8a01c840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #12 0x564b8a073269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #13 0x564b8a01c840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #14 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #15 0x564b8a06e60a in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567:11 #16 0x7f5ea0f0ff40 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154:19 #17 0x564b8a133853 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348:13 #18 0x564b8a038a1f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085:12 #19 0x564b8a01dd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #20 0x564b8a01c301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #21 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #22 0x564b8a063c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #23 0x564b8a01f3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #24 0x564b8a134e97 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687:10 #25 0x564b8a07cd49 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4191:14 #26 0x564b8a250a0a in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:671:16 #27 0x564b8a25db2f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264:8 #28 0x564b8a01c840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #29 0x564b8a01c541 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1219:19 #30 0x564b8a073269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 previously allocated by thread T0 here: #0 0x564b89daebb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x564b8a0f8c7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x564b89e5132b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x564b89e5132b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7b5e9349c0ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x564b89f66365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x564b8a02a77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x564b8a01dd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x564b8a01c301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x564b8a063c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x564b8a01f3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x564b8a12ae14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x564b8a129a98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x564b8a12c073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x564b8a02ff93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x564b8a01dd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x564b8a01c301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x564b8a063c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x564b8a01f3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x564b8a01cd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x564b8a07a653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x564b8a02a77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x564b8a01dd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x564b8a01c301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x564b8a064a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x564b8a063c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x564b8a01f3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x564b8a01cd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x564b8a075bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7daeae2c0680: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7daeae2c0700: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7daeae2c0780: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7daeae2c0800: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7daeae2c0880: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7daeae2c0900: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7daeae2c0980: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7daeae2c0a00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7daeae2c0a80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7daeae2c0b00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7daeae2c0b80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==474479==ABORTING Running the tests in ‘tests/drop.R’ failed. Complete output: > if (.Platform$OS.type != "windows") withAutoprint({ + library(lme4) + + fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) + + ## slightly weird model but plausible --- not that + ## one would want to try drop1() on this model ... + fm2 <- lmer(Reaction ~ 1+ (Days|Subject), sleepstudy) + drop1(fm2) ## empty + update(fm1, . ~ . - Days) + anova(fm2) ## empty + + terms(fm1) + terms(fm1,fixed.only=FALSE) + + extractAIC(fm1) + + drop1(fm1) + drop1(fm1, test="Chisq") + + gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), + family = binomial, data = cbpp, nAGQ=25L) + + drop1(gm1, test="Chisq") + + }) ## skip on windows (for speed) > library(lme4) Loading required package: Matrix > fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) > fm2 <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) > drop1(fm2) Single term deletions Model: Reaction ~ 1 + (Days | Subject) npar AIC 1 1785.5 > update(fm1, . ~ . - Days) Linear mixed model fit by REML ['lmerMod'] Formula: Reaction ~ (Days | Subject) Data: sleepstudy REML criterion at convergence: 1769.845 Random effects: Groups Name Std.Dev. Corr Subject (Intercept) 25.53 Days 11.93 -0.18 Residual 25.59 Number of obs: 180, groups: Subject, 18 Fixed Effects: (Intercept) 257.8 > anova(fm2) Analysis of Variance Table npar Sum Sq Mean Sq F value > terms(fm1) Reaction ~ Days attr(,"variables") list(Reaction, Days) attr(,"factors") Days Reaction 0 Days 1 attr(,"term.labels") [1] "Days" attr(,"order") [1] 1 attr(,"intercept") [1] 1 attr(,"response") [1] 1 attr(,".Environment") attr(,"predvars") list(Reaction, Days) > terms(fm1, fixed.only = FALSE) Reaction ~ Days + (Days + Subject) attr(,"variables") list(Reaction, Days, Subject) attr(,"factors") Days Subject Reaction 0 0 Days 1 0 Subject 0 1 attr(,"term.labels") [1] "Days" "Subject" attr(,"order") [1] 1 1 attr(,"intercept") [1] 1 attr(,"response") [1] 1 attr(,".Environment") attr(,"predvars") list(Reaction, Days, Subject) attr(,"dataClasses") Reaction Days Subject "numeric" "numeric" "factor" attr(,"predvars.fixed") list(Reaction, Days) attr(,"varnames.fixed") [1] "Reaction" "Days" attr(,"predvars.random") list(Reaction, Days, Subject) > extractAIC(fm1) [1] 6.000 1763.939 > drop1(fm1) Single term deletions Model: Reaction ~ Days + (Days | Subject) npar AIC 1763.9 Days 1 1785.5 > drop1(fm1, test = "Chisq") Single term deletions Model: Reaction ~ Days + (Days | Subject) npar AIC LRT Pr(Chi) 1763.9 Days 1 1785.5 23.537 1.226e-06 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), + family = binomial, data = cbpp, nAGQ = 25L) ================================================================= ==509316==ERROR: AddressSanitizer: heap-use-after-free on address 0x7d97c07af8b0 at pc 0x7bd7ac5fb93c bp 0x7ffc740342d0 sp 0x7ffc740342c8 READ of size 16 at 0x7d97c07af8b0 thread T0 #0 0x7bd7ac5fb93b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7bd7ac5fb93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7bd7ac5fb93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7bd7ac5fb93b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7bd7ac5fb93b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7bd7ac5fb93b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7bd7ac5fb93b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7bd7ac5fb93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7bd7ac5fb93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7bd7ac5fb93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7bd7ac5fb93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7bd7ac5fb93b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7bd7ac589cd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7bd7ac589cd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7bd7ac58c47e in glmerAGQ /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:428:9 #15 0x55ef29553f2e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #16 0x55ef29617d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x55ef296013be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x55ef295fed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x55ef29657bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x55ef295fe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x55ef29655269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x55ef295fe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x55ef2961feba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x55ef2961feba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x55ef2960060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x55ef295fe4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x55ef296009a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x55ef295fe9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x55ef29657bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x55ef295fe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x55ef296009a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x55ef295fe9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x55ef296009a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x55ef295fe9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x55ef2960060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x55ef295fe2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x55ef2960c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x55ef296013be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x55ef295fed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x55ef29655269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x55ef295fe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x55ef2961feba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x55ef2961feba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x55ef296013be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x55ef295fed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x55ef294b4abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x55ef2960c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x55ef296013be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x55ef295fed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x55ef29657bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x55ef295fe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x55ef2965cfba in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993:9 #75 0x55ef2960c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #76 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #77 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #78 0x55ef2960060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #79 0x55ef295fe4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #80 0x55ef2965d883 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018:9 #81 0x55ef297064b9 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11 #82 0x55ef29611f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #83 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #84 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #85 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #86 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #87 0x55ef296013be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #88 0x55ef295fed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #89 0x55ef295fe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #90 0x55ef296cfbe1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #91 0x55ef296d2410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #92 0x55ef296d2410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #93 0x55ef296d24a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #94 0x55ef293d3d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #95 0x7fd7c3c12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #96 0x7fd7c3c12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #97 0x55ef292eb7d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7d97c07af8b0 is located 48 bytes inside of 1840-byte region [0x7d97c07af880,0x7d97c07affb0) freed by thread T0 here: #0 0x55ef29390916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x55ef296ed31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x55ef296ed31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x55ef296e018b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x55ef296dd195 in Rf_cons /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2488:2 #5 0x55ef2983292f in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:667:9 #6 0x55ef2983fb2f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264:8 #7 0x55ef295fe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #8 0x55ef295fe541 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1219:19 #9 0x55ef29655269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #10 0x55ef295fe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #11 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #12 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #13 0x55ef2961feba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #14 0x55ef2961feba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #15 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #16 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #17 0x55ef2960060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #18 0x55ef295fe4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #19 0x55ef296009a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #20 0x55ef295fe9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #21 0x55ef29657bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #22 0x55ef295fe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #23 0x55ef296009a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #24 0x55ef295fe9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #25 0x55ef296009a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #26 0x55ef295fe9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #27 0x55ef2960060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #28 0x55ef295fe2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #29 0x55ef2960c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #30 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #31 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 previously allocated by thread T0 here: #0 0x55ef29390bb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x55ef296dac7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x55ef2943332b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x55ef2943332b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7bd7b30d80ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x55ef29548365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x55ef2960c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x55ef296013be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x55ef2970ce14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x55ef2970ba98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x55ef2970e073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x55ef29611f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x55ef296013be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x55ef295fed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x55ef2965c653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x55ef2960c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x55ef295ffd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x55ef295fe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x55ef29646a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x55ef29645c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x55ef296013be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x55ef295fed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x55ef29657bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7d97c07af600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d97c07af680: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d97c07af700: fd fd fd fd fd fd fd fd fd fd fd fa fa fa fa fa 0x7d97c07af780: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d97c07af800: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d97c07af880: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7d97c07af900: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d97c07af980: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d97c07afa00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d97c07afa80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d97c07afb00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==509316==ABORTING Running the tests in ‘tests/glmer-1.R’ failed. Complete output: > if (lme4:::testLevel() > 1 || .Platform$OS.type!="windows") withAutoprint({ + + ## generalized linear mixed model + stopifnot(suppressPackageStartupMessages(require(lme4))) + options(show.signif.stars = FALSE) + + source(system.file("test-tools-1.R", package = "Matrix"), keep.source = FALSE) + ## + ##' Check that coefficient +- "2" * SD contains true value + ##' + ##' @title Check that confidence interval for coefficients contains true value + ##' @param fm fitted model, e.g., from lm(), lmer(), glmer(), .. + ##' @param true.coef numeric vector of true (fixed effect) coefficients + ##' @param conf.level confidence level for confidence interval + ##' @param sd.factor the "2", i.e. default 1.96 factor for the confidence interval + ##' @return TRUE or a string of "error" + ##' @author Martin Maechler + chkFixed <- function(fm, true.coef, conf.level = 0.95, + sd.factor = qnorm((1+conf.level)/2)) + { + stopifnot(is.matrix(cf <- coefficients(summary(fm))), ncol(cf) >= 2) + cc <- cf[,1] + sd <- cf[,2] + if(any(out1 <- true.coef < cc - sd.factor*sd)) + return(sprintf("true coefficient[j], j=%s, is smaller than lower confidence limit", + paste(which(out1), collapse=", "))) + if(any(out2 <- true.coef > cc + sd.factor*sd)) + return(sprintf("true coefficient[j], j=%s, is larger than upper confidence limit", + paste(which(out2), collapse=", "))) + ## else, return + TRUE + } + + + ## TODO: (1) move these to ./glmer-ex.R [DONE] + ## ---- (2) "rationalize" with ../man/cbpp.Rd + #m1e <- glmer1(cbind(incidence, size - incidence) ~ period + (1 | herd), + # family = binomial, data = cbpp, doFit = FALSE) + ## now + #bobyqa(m1e, control = list(iprint = 2L)) + + m1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), + family = binomial, data = cbpp) + m1. <- update(m1, start = getME(m1, c("theta", "fixef"))) + dm1 <- drop1(m1) + stopifnot(all.equal(drop1(m1.), dm1, tol = 1e-10))# Lnx(F28) 64b: 4e-12 + ## response as a vector of probabilities and usage of argument "weights" + m1p <- glmer(incidence / size ~ period + (1 | herd), weights = size, + family = binomial, data = cbpp) + ## Confirm that these are equivalent: + stopifnot(all.equal(fixef(m1), fixef(m1p)), + all.equal(ranef(m1), ranef(m1p)), + TRUE) + ## for(m in c(m1, m1p)) { + ## cat("-------\\n\\nCall: ", + ## paste(format(getCall(m)), collapse="\\n"), "\\n") + ## print(logLik(m)); cat("AIC:", AIC(m), "\\n") ; cat("BIC:", BIC(m),"\\n") + ## } + stopifnot(all.equal(logLik(m1), logLik(m1p)), + all.equal(AIC(m1), AIC(m1p)), + all.equal(BIC(m1), BIC(m1p))) + + + ## changed tolPwrss to 1e-7 to match other default + m1b <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), + family = binomial, data = cbpp, verbose = 2L, + control = + glmerControl(optimizer="bobyqa", tolPwrss=1e-7, + optCtrl=list(rhobeg=0.2, rhoend=2e-7))) + + ## using nAGQ=9L provides a better evaluation of the deviance + m.9 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), + family = binomial, data = cbpp, nAGQ = 9) + + ## check with nAGQ = 25 + m2 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), + family = binomial, data = cbpp, nAGQ = 25) + + ## loosened tolerance on parameters + stopifnot(is((cm2 <- coef(m2)), "coef.mer"), + dim(cm2$herd) == c(15,4), + all.equal(fixef(m2), + ### lme4a [from an Ubuntu 11.10 amd64 system] + c(-1.39922533406847, -0.991407294757321, + -1.12782184600404, -1.57946627431248), + ##c(-1.3766013, -1.0058773, + ## -1.1430128, -1.5922817), + tolerance = 5.e-4, + check.attributes=FALSE), + all.equal(c(-2*logLik(m2)), 100.010030538022, tolerance=1e-9), + all.equal(deviance(m2), 73.373, tolerance=1e-5) + ## with bobyqa first (AGQ=0), then + ##all.equal(deviance(m2), 101.119749563, tolerance=1e-9) + ) + + ## 32-bit Ubuntu 10.04: + coef_m1_lme4.0 <- structure(c(-1.39853505102576, + -0.992334712470269, -1.12867541092127, + -1.58037389566025), + .Names = c("(Intercept)", "period2", "period3", + "period4")) + + ## library(glmmADMB) + ## mg <- glmmadmb(cbind(incidence, size - incidence) ~ period + (1 | herd), + ## family = "binomial", data = cbpp) + coef_m1_glmmadmb <- structure(c(-1.39853810064827, -0.99233330126975, -1.12867317840779, + -1.58031150854503), .Names = c("(Intercept)", "period2", "period3", + "period4")) + + ## library(glmmML) + ## mm <- glmmML(cbind(incidence, size - incidence) ~ period, + ## cluster=herd, + ## family = "binomial", data = cbpp) + coef_m1_glmmML <- structure(c(-1.39853234657711, -0.992336901732793, -1.12867036466201, + -1.58030977686564), .Names = c("(Intercept)", "period2", "period3", + "period4")) + + ## lme4[r 1636], 64-bit ubuntu 11.10: + ## c(-1.3788385, -1.0589543, + ## -1.1936382, -1.6306271), + + stopifnot(is((cm1 <- coef(m1b)), "coef.mer"), + dim(cm1$herd) == c(15,4), + all.equal(fixef(m1b),fixef(m1),tolerance=4e-5), + is.all.equal4(fixef(m1b), + coef_m1_glmmadmb, + coef_m1_lme4.0, + coef_m1_glmmML, + tol = 5e-4) + ) + + + ## Deviance for the new algorithm is lower, eventually we should change the previous test + ##stopifnot(deviance(m1) <= deviance(m1e)) + + showProc.time() # + + if (require('MASS', quietly = TRUE)) { + bacteria$wk2 <- bacteria$week > 2 + contrasts(bacteria$trt) <- + structure(contr.sdif(3), + dimnames = list(NULL, c("diag", "encourage"))) + print(fm5 <- glmer(y ~ trt + wk2 + (1|ID), + data=bacteria, family=binomial)) + showProc.time() # + + stopifnot( + all.equal(logLik(fm5), + ## was -96.127838 + structure(-96.13069, nobs = 220L, nall = 220L, + df = 5L, REML = FALSE, + class = "logLik"), + tolerance = 5e-4, check.attributes = FALSE) + , + all.equal(fixef(fm5), + ## was 2.834218798 -1.367099481 + c("(Intercept)"= 2.831609490, "trtdiag"= -1.366722631, + ## now 0.5842291915, -1.599148773 + "trtencourage"=0.5840147802, "wk2TRUE"=-1.598591346), + tolerance = 1e-4 ) + ) + } + + ## Failure to specify a random effects term - used to give an obscure message + ## Ensure *NON*-translated message; works on Linux,... : + if(.Platform$OS.type == "unix") { + Sys.setlocale("LC_MESSAGES", "C") + tc <- tryCatch( + m2 <- glmer(incidence / size ~ period, weights = size, + family = binomial, data = cbpp) + , error = function(.) .) + stopifnot(inherits(tc, "error"), + identical(tc$message, + "No random effects terms specified in formula")) + } + + + ## glmer - Modeling overdispersion as "mixture" aka + ## ----- - *ONE* random effect *PER OBSERVATION" -- example inspired by Ben Bolker: + + ##' + ##' + ##'
+ ##' @title + ##' @param ng number of groups + ##' @param nr number of "runs", i.e., observations per groups + ##' @param sd standard deviations of group and "Individual" random effects, + ##' (\sigma_f, \sigma_I) + ##' @param b true beta (fixed effects) + ##' @return a data frame (to be used in glmer()) with columns + ##' (x, f, obs, eta0, eta, mu, y), where y ~ Pois(lambda(x)), + ##' log(lambda(x_i)) = b_1 + b_2 * x + G_{f(i)} + I_i + ##' and G_k ~ N(0, \sigma_f); I_i ~ N(0, \sigma_I) + ##' @author Ben Bolker and Martin Maechler + rPoisGLMMi <- function(ng, nr, sd=c(f = 1, ind = 0.5), b=c(1,2)) + { + stopifnot(nr >= 1, ng >= 1, + is.numeric(sd), names(sd) %in% c("f","ind"), sd >= 0) + ntot <- nr*ng + b.reff <- rnorm(ng, sd= sd[["f"]]) + b.rind <- rnorm(ntot,sd= sd[["ind"]]) + x <- runif(ntot) + within(data.frame(x, + f = factor(rep(LETTERS[1:ng], each=nr)), + obs = 1:ntot, + eta0 = cbind(1, x) %*% b), + { + eta <- eta0 + b.reff[f] + b.rind[obs] + mu <- exp(eta) + y <- rpois(ntot, lambda=mu) + }) + } + + set.seed(1) + dd <- rPoisGLMMi(12, 20) + m0 <- glmer(y~x + (1|f), family="poisson", data=dd) + m1 <- glmer(y~x + (1|f) + (1|obs), family="poisson", data=dd) + stopifnot(isTRUE(chkFixed(m0, true.coef = c(1,2))), + isTRUE(chkFixed(m1, true.coef = c(1,2)))) + (a01 <- anova(m0, m1)) + + stopifnot(all.equal(a01$Chisq[2], 554.334056, tolerance=1e-5), + all.equal(a01$logLik, c(-1073.77193, -796.604902), tolerance=1e-6), + a01$ npar == 3:4, + na.omit(a01$ Df) == 1) + + if(lme4:::testLevel() > 1) { + nsim <- 10 + set.seed(2) + system.time( + simR <- lapply(1:nsim, function(i) { + cat(i,"", if(i %% 20 == 0)"\n") + dd <- rPoisGLMMi(10 + rpois(1, lambda=3), + 16 + rpois(1, lambda=5)) + m0 <- glmer(y~x + (1|f), family="poisson", data=dd) + m1 <- glmer(y~x + (1|f) + (1|obs), family="poisson", data=dd) + a01 <- anova(m0, m1) + stopifnot(a01$ npar == 3:4, + na.omit(a01$ Df) == 1) + list(chk0 = chkFixed(m0, true.coef = c(1,2)), + chk1 = chkFixed(m1, true.coef = c(1,2)), + chisq= a01$Chisq[2], + lLik = a01$logLik) + })) + + ## m0 is the wrong model, so we don't expect much here: + table(unlist(lapply(simR, `[[`, "chk0"))) + + + ## If the fixed effect estimates were unbiased and the standard errors correct, + ## and N(0,sigma^2) instead of t_{nu} good enough for the fixed effects, + ## the confidence interval should contain the true coef in ~95 out of 100: + table(unlist(lapply(simR, `[[`, "chk1"))) + + ## The tests are all highly significantly in favor of m1 : + summary(chi2s <- sapply(simR, `[[`, "chisq")) + ## Min. 1st Qu. Median Mean 3rd Qu. Max. + ## 158.9 439.0 611.4 698.2 864.3 2268.0 + stopifnot(chi2s > qchisq(0.9999, df = 1)) + } + + showProc.time() + }) ## skip if windows and testLevel<1 > stopifnot(suppressPackageStartupMessages(require(lme4))) > options(show.signif.stars = FALSE) > source(system.file("test-tools-1.R", package = "Matrix"), keep.source = FALSE) Loading required package: tools > chkFixed <- function(fm, true.coef, conf.level = 0.95, sd.factor = qnorm((1 + + conf.level)/2)) { + stopifnot(is.matrix(cf <- coefficients(summary(fm))), ncol(cf) >= 2) + cc <- cf[, 1] + sd <- cf[, 2] + if (any(out1 <- true.coef < cc - sd.factor * sd)) + return(sprintf("true coefficient[j], j=%s, is smaller than lower confidence limit", + paste(which(out1), collapse = ", "))) + if (any(out2 <- true.coef > cc + sd.factor * sd)) + return(sprintf("true coefficient[j], j=%s, is larger than upper confidence limit", + paste(which(out2), collapse = ", "))) + TRUE + } > m1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), + family = binomial, data = cbpp) ================================================================= ==535996==ERROR: AddressSanitizer: heap-use-after-free on address 0x7d12853a40b0 at pc 0x7b52712ce93c bp 0x7ffd0357fd10 sp 0x7ffd0357fd08 READ of size 16 at 0x7d12853a40b0 thread T0 #0 0x7b52712ce93b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7b52712ce93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7b52712ce93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7b52712ce93b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7b52712ce93b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7b52712ce93b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7b52712ce93b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7b52712ce93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7b52712ce93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7b52712ce93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7b52712ce93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7b52712ce93b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7b527125ccd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7b527125ccd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7b527125bbc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x55d055484b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x55d055548d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x55d0555323be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x55d05552fd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x55d055588bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x55d05552f840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x55d055586269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x55d05552f840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x55d055550eba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x55d055550eba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x55d05553160a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x55d05552f4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x55d0555319a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x55d05552f9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x55d055588bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x55d05552f840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x55d0555319a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x55d05552f9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x55d0555319a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x55d05552f9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x55d05553160a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x55d05552f2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x55d05553d77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x55d0555323be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x55d05552fd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x55d055586269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x55d05552f840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x55d055550eba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x55d055550eba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x55d0555323be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x55d05552fd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x55d0553e5abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x55d05553d77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x55d0555323be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x55d05552fd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x55d055588bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x55d05552f840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x55d05558dfba in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993:9 #75 0x55d05553d77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #76 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #77 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #78 0x55d05553160a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #79 0x55d05552f4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #80 0x55d05558e883 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018:9 #81 0x55d0556374b9 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11 #82 0x55d055542f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #83 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #84 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #85 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #86 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #87 0x55d0555323be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #88 0x55d05552fd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #89 0x55d05552f840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #90 0x55d055600be1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #91 0x55d055603410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #92 0x55d055603410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #93 0x55d0556034a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #94 0x55d055304d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #95 0x7f5288911574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #96 0x7f5288911627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #97 0x55d05521c7d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7d12853a40b0 is located 48 bytes inside of 1840-byte region [0x7d12853a4080,0x7d12853a47b0) freed by thread T0 here: #0 0x55d0552c1916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x55d05561e31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x55d05561e31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x55d05561118b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x55d055626fc5 in CONS_NR /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2519:2 #5 0x55d055541cfa in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8059:21 #6 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #7 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #8 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #9 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #10 0x55d0555323be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #11 0x55d05552fd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #12 0x55d0555819cb in do_if /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2709:20 #13 0x55d05552f840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #14 0x55d055586269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #15 0x55d05552f840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #16 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #17 0x55d05558160a in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567:11 #18 0x7f52857e9f40 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154:19 #19 0x55d055646853 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348:13 #20 0x55d05554ba1f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085:12 #21 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #22 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #23 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #24 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #25 0x55d0555323be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #26 0x55d055647e97 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687:10 #27 0x55d05558fd49 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4191:14 #28 0x55d055763a0a in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:671:16 #29 0x55d055770b2f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264:8 #30 0x55d05552f840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 previously allocated by thread T0 here: #0 0x55d0552c1bb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x55d05560bc7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x55d05536432b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x55d05536432b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7b5277e9c0ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x55d055479365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x55d05553d77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x55d0555323be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x55d05563de14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x55d05563ca98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x55d05563f073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x55d055542f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x55d0555323be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x55d05552fd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x55d05558d653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x55d05553d77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x55d055530d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x55d05552f301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x55d055577a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x55d055576c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x55d0555323be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x55d05552fd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x55d055588bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7d12853a3e00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d12853a3e80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d12853a3f00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d12853a3f80: 00 00 00 00 00 00 00 00 00 00 00 fa fa fa fa fa 0x7d12853a4000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d12853a4080: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7d12853a4100: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d12853a4180: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d12853a4200: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d12853a4280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d12853a4300: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==535996==ABORTING Running the tests in ‘tests/glmerControlPass.R’ failed. Complete output: > if (.Platform$OS.type != "windows") { + ## test redirection from lmer to glmer (correct options passed, + ## specifically glmerControl -> tolPwrss + + library("lme4") + library("testthat") + ## data("trees513", package = "multcomp") + load(system.file("testdata","trees513.RData",package="lme4")) + + + expect_is(mmod1 <- glmer(damage ~ species - 1 + (1 | lattice / plot), + data = trees513B, family = binomial()),"glmerMod") + if(FALSE) { ## Now (2019-05) defunct; was deprecated since 2013-06: + expect_warning(mmod2 <- lmer(damage ~ species - 1 + (1 | lattice / plot), + data = trees513B, family = binomial()), + "calling lmer with .* is deprecated") + mmod2@call <- mmod1@call ## hack calls to equality + expect_equal(mmod1,mmod2) + } + } ## skip on windows (for speed) Loading required package: Matrix ================================================================= ==538173==ERROR: AddressSanitizer: heap-use-after-free on address 0x7f0fbb900830 at pc 0x7bcfa791593c bp 0x7ffe4edf57d0 sp 0x7ffe4edf57c8 READ of size 16 at 0x7f0fbb900830 thread T0 #0 0x7bcfa791593b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7bcfa791593b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7bcfa791593b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7bcfa791593b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7bcfa791593b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7bcfa791593b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7bcfa791593b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7bcfa791593b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7bcfa791593b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7bcfa791593b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7bcfa791593b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7bcfa791593b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7bcfa78a3cd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7bcfa78a3cd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7bcfa78a2bc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x55750dee2b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x55750dfa6d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x55750df8dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x55750dfe6bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x55750df8d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x55750dfe4269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x55750df8d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x55750dfaeeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x55750dfaeeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x55750df8f60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x55750df8d4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x55750df8f9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x55750df8d9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x55750dfe6bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x55750df8d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x55750df8f9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x55750df8d9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x55750df8f9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x55750df8d9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x55750df8f60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x55750df8d2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x55750df9b77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x55750df8dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x55750dfe4269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x55750df8d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x55750dfaeeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x55750dfaeeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x55750df8dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x55750de43abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x55750df9b77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x55750df8dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x55750dfe6bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x55750df8d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x55750ded7365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #75 0x55750df9b77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #76 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #77 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #78 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #79 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #80 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #81 0x55750df8dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #82 0x55750dfe4269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #83 0x55750df8d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #84 0x55750df8d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #85 0x55750e05ebe1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #86 0x55750e061410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #87 0x55750e061410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #88 0x55750e0614a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #89 0x55750dd62d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #90 0x7fcfbef11574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #91 0x7fcfbef11627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #92 0x55750dc7a7d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7f0fbb900830 is located 48 bytes inside of 129024-byte region [0x7f0fbb900800,0x7f0fbb920000) freed by thread T0 here: #0 0x55750dd1f916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x55750e07c31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x55750e07c31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x55750e06f18b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x55750e0860e5 in Rf_mkPROMISE /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2613:2 #5 0x55750dfd5136 in make_applyClosure_env /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2280:16 #6 0x55750dfd4b25 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2304:19 #7 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #8 0x55750df8dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #9 0x55750df8d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #10 0x55750dfe4269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #11 0x55750df8d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #12 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #13 0x55750dfdf60a in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567:11 #14 0x7fcfbbf35f40 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154:19 #15 0x55750e0a4853 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348:13 #16 0x55750dfa9a1f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085:12 #17 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x55750e0a5e97 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687:10 #23 0x55750dfcda0f in tryDispatch /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6090:16 #24 0x55750df9b1c2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8320:19 #25 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #26 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #27 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x55750df8dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 previously allocated by thread T0 here: #0 0x55750dd1fbb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x55750e069c7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x55750ddc232b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x55750ddc232b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7bcfae49c0ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x55750ded7365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x55750df9b77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x55750e09be14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x55750e09aa98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x55750e09d073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x55750dfa0f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x55750df8dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x55750dfeb653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x55750df9b77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x55750df8ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x55750df8d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x55750dfd5a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x55750dfd4c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x55750df903be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x55750df8dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x55750dfe6bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7f0fbb900580: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7f0fbb900600: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7f0fbb900680: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7f0fbb900700: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7f0fbb900780: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7f0fbb900800: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7f0fbb900880: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7f0fbb900900: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7f0fbb900980: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7f0fbb900a00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7f0fbb900a80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==538173==ABORTING Running the tests in ‘tests/glmmExt.R’ failed. Complete output: > ## Tests of a variety of GLMM families and links > ## coding: family {g=Gamma, P=Poisson, G=Gaussian, B=binomial} > ## link {l=log, i=inverse, c=cloglog, i=identity} > ## model {1 = intercept-only, 2 = with continuous predictor} > > library("lme4") Loading required package: Matrix > > source(system.file("testdata/lme-tst-funs.R", package="lme4", mustWork=TRUE)) > ##-> gSim(), a general simulation function ... > > str(gSim) function (nblk = 26, nperblk = 100, sigma_B = 1, beta = c(4, 3), x = runif(n), shape = 2, nbinom = 10, sd = 1, dInitial = NULL, family = Gamma()) > ## function (nblk = 26, nperblk = 100, sigma = 1, beta = c(4, 3), > ## x = runif(n), shape = 2, nbinom = 10, family = Gamma()) > > if (.Platform$OS.type != "windows") withAutoprint({ + set.seed(101) + ## Gamma, inverse link (= default) : + d <- gSim() + ## Gamma, log link eta = log(mu) : + dgl <- gSim(dInitial = d, family = Gamma(link = log)) + ## Poisson, log link + dP <- gSim(dInitial = d, family = poisson()) + ## Gaussian, log link --- need to use a non-identity link, otherwise glmer calls lmer + dG <- gSim(dInitial = d, family = gaussian(link = log), sd = 2) + ## Gaussian with inverse link : (sd small enough to avoid negative values) : + dGi <- gSim(dInitial = d, family = gaussian(link = inverse), sd = 0.01) + ## binomial with cloglog link + dBc <- d + dBc$eta <- d$eta - 5 # <==> beta intercept 5 less: otherwise y will be constant + dBc <- gSim(dInitial = dBc, ## beta = c(-1, 3), + nbinom = 1, family = binomial(link="cloglog")) + + ## binomial with identity link + dBi <- d + dBc$eta <- d$eta / 10 # <==> beta slope / 10 : scale so range goes from 0.2-0.8 + dBi <- gSim(dInitial = dBc, ## beta = c(4, 3/10), + nbinom = 1, family = binomial(link="identity")) + + + ############ + ## Gamma/inverse + + ## GLMs + gm0 <- glm(y ~ 1, data=d, family=Gamma) + gm1 <- glm(y ~ block-1, data=d, family=Gamma) + stopifnot(all.equal(sd(coef(gm1)),1.00753942148611)) + + gm2 <- glmer(y ~ 1 + (1|block), d, Gamma, nAGQ=0) + gm3 <- glmer(y ~ x + (1|block), d, Gamma, nAGQ=0) + gm2B <- glmer(y ~ 1 + (1|block), d, Gamma) + gm3B <- glmer(y ~ x + (1|block), d, Gamma) + + ## y ~ x + (1|block), Gamma is TRUE model + summary(gm3) + summary(gm3B)# should be better + ## Both have "correct" beta ~= (4, 3) -- but *too* small (sigma_B, sigma) !! + stopifnot(exprs = { + all.equal(fixef(gm3 ), c(`(Intercept)` = 4.07253, x = 3.080585), tol = 1e-5) # 1.21e-7 + all.equal(fixef(gm3B), c(`(Intercept)` = 4.159398, x = 3.058521),tol = 1e-5) # 1.13e-7 + }) + VarCorr(gm3) # both variances / std.dev. should be ~ 1 but are too small + + + + ## + ## library(hglm) + ## h1 <- hglm2(y~x+(1|block), data=d, family=Gamma()) + ## lme4.0 fails on all of these ... + + ## Gamma/log + ggl1 <- glmer(y ~ 1 + (1|block), data=dgl, family=Gamma(link="log")) + ggl2 <- glmer(y ~ x + (1|block), data=dgl, family=Gamma(link="log"))# true model + (h.1.2 <- anova(ggl1, ggl2)) + stopifnot( + all.equal(unlist(h.1.2[2,]), + c(npar = 4, AIC = 34216.014, BIC = 34239.467, logLik = -17104.007, + "-2*log(L)" = 34208.014, Chisq = 2458.5792, Df = 1, `Pr(>Chisq)` = 0)) + ) + ## "true" model : + summary(ggl2) + VarCorr(ggl2) + + ## + ## library(lme4.0) + ## ggl1 <- glmer(y ~ 1 + (1|block), data=dgl, family=Gamma(link="log"), verbose= 2) + ## fails + + ## Poisson/log + gP1 <- glmer(y ~ 1 + (1|block), data=dP, family=poisson) + gP2 <- glmer(y ~ x + (1|block), data=dP, family=poisson) + + ## Gaussian/log + gG1 <- glmer(y ~ 1 + (1|block), data=dG, family=gaussian(link="log")) + gG2 <- glmer(y ~ x + (1|block), data=dG, family=gaussian(link="log")) + + ## works with lme4.0 but AIC/BIC/logLik are crazy, and scale + ## parameter is not reported + ## glmmML etc. doesn't allow models with scale parameters + ## gG1B <- glmmadmb(y ~ 1 + (1|block), data=dG, + ## family="gaussian",link="log",verbose=TRUE) + ## what is the best guess at the estimate of the scale parameter? + ## is it the same as sigma? + ## gG1B$alpha + + ## if(Sys.info()["user"] != "maechler") { # <- seg.faults (MM) + + ## Gaussian/inverse + gGi1 <- glmer(y ~ 1 + (1|block), data=dGi, family=gaussian(link="inverse")) + gGi2 <- glmer(y ~ x + (1|block), data=dGi, family=gaussian(link="inverse")) + + + ## Binomial/cloglog + gBc1 <- glmer(y ~ 1 + (1|block), data=dBc, family=binomial(link="cloglog")) + gBc2 <- glmer(y ~ x + (1|block), data=dBc, family=binomial(link="cloglog")) + ## library("glmmADMB") + ## glmmadmbfit <- glmmadmb(y ~ x + (1|block), data=dBc, + ## family="binomial",link="cloglog") + glmmadmbfit <- list(fixef = c("(Intercept)" = -0.717146132730349, x =2.83642900561633), + VarCorr = structure(list( + block = structure(0.79992, .Dim = c(1L, 1L), + .Dimnames = list("(Intercept)", "(Intercept)"))), + class = "VarCorr")) + stopifnot(all.equal(fixef(gBc2), glmmadmbfit$fixef, tolerance=5e-3)) + ## pretty loose tolerance ... + stopifnot(all.equal(unname(unlist(VarCorr(gBc2))), + c(glmmadmbfit$VarCorr$block), tolerance=2e-2)) + + gBi1 <- glmer(y ~ 1 + (1|block), data=dBi, family=binomial(link="identity")) + gBi2 <- glmer(y ~ x + (1|block), data=dBi, family=binomial(link="identity")) + + ## FIXME: should test more of the *results* of these efforts, not + ## just that they run without crashing ... + }) ## skip on windows (for speed) > set.seed(101) > d <- gSim() > dgl <- gSim(dInitial = d, family = Gamma(link = log)) > dP <- gSim(dInitial = d, family = poisson()) > dG <- gSim(dInitial = d, family = gaussian(link = log), sd = 2) > dGi <- gSim(dInitial = d, family = gaussian(link = inverse), sd = 0.01) > dBc <- d > dBc$eta <- d$eta - 5 > dBc <- gSim(dInitial = dBc, nbinom = 1, family = binomial(link = "cloglog")) > dBi <- d > dBc$eta <- d$eta/10 > dBi <- gSim(dInitial = dBc, nbinom = 1, family = binomial(link = "identity")) > gm0 <- glm(y ~ 1, data = d, family = Gamma) > gm1 <- glm(y ~ block - 1, data = d, family = Gamma) > stopifnot(all.equal(sd(coef(gm1)), 1.00753942148611)) > gm2 <- glmer(y ~ 1 + (1 | block), d, Gamma, nAGQ = 0) > gm3 <- glmer(y ~ x + (1 | block), d, Gamma, nAGQ = 0) > gm2B <- glmer(y ~ 1 + (1 | block), d, Gamma) > gm3B <- glmer(y ~ x + (1 | block), d, Gamma) > summary(gm3) Generalized linear mixed model fit by maximum likelihood (Adaptive Gauss-Hermite Quadrature, nAGQ = 0) [glmerMod] Family: Gamma ( inverse ) Formula: y ~ x + (1 | block) Data: d AIC BIC logLik -2*log(L) df.resid -4243.7 -4220.3 2125.9 -4251.7 2596 Scaled residuals: Min 1Q Median 3Q Max -1.4253 -0.7327 -0.2273 0.4677 5.8018 Random effects: Groups Name Variance Std.Dev. block (Intercept) 1.104 1.051 Number of obs: 2600, groups: block, 26 Fixed effects: Estimate Std. Error t value Pr(>|z|) (Intercept) 4.0725 0.1895 21.49 <2e-16 *** x 3.0806 0.2491 12.37 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Correlation of Fixed Effects: (Intr) x -0.531 > summary(gm3B) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) [glmerMod] Family: Gamma ( inverse ) Formula: y ~ x + (1 | block) Data: d AIC BIC logLik -2*log(L) df.resid -4243.9 -4220.4 2125.9 -4251.9 2596 Scaled residuals: Min 1Q Median 3Q Max -1.4213 -0.7290 -0.2248 0.4725 5.7931 Random effects: Groups Name Variance Std.Dev. block (Intercept) 1.097 1.047 Number of obs: 2600, groups: block, 26 Fixed effects: Estimate Std. Error t value Pr(>|z|) (Intercept) 4.1594 0.2325 17.89 <2e-16 *** x 3.0585 0.2481 12.33 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Correlation of Fixed Effects: (Intr) x -0.432 > stopifnot(exprs = { + all.equal(fixef(gm3), c(`(Intercept)` = 4.07253, x = 3.080585), tol = 1e-05) + all.equal(fixef(gm3B), c(`(Intercept)` = 4.159398, x = 3.058521), tol = 1e-05) + }) > VarCorr(gm3) Groups Name Std.Dev. block (Intercept) 1.0505 > ggl1 <- glmer(y ~ 1 + (1 | block), data = dgl, family = Gamma(link = "log")) > ggl2 <- glmer(y ~ x + (1 | block), data = dgl, family = Gamma(link = "log")) > (h.1.2 <- anova(ggl1, ggl2)) Data: dgl Models: ggl1: y ~ 1 + (1 | block) ggl2: y ~ x + (1 | block) npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) ggl1 3 36673 36690 -18333 36667 ggl2 4 34216 34239 -17104 34208 2458.6 1 < 2.2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > stopifnot(all.equal(unlist(h.1.2[2, ]), c(npar = 4, AIC = 34216.014, BIC = 34239.467, + logLik = -17104.007, `-2*log(L)` = 34208.014, Chisq = 2458.5792, Df = 1, `Pr(>Chisq)` = 0))) > summary(ggl2) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) [glmerMod] Family: Gamma ( log ) Formula: y ~ x + (1 | block) Data: dgl AIC BIC logLik -2*log(L) df.resid 34216.0 34239.5 -17104.0 34208.0 2596 Scaled residuals: Min 1Q Median 3Q Max -1.4203 -0.7299 -0.2377 0.5233 5.0699 Random effects: Groups Name Variance Std.Dev. block (Intercept) 0.8163 0.9035 Number of obs: 2600, groups: block, 26 Fixed effects: Estimate Std. Error t value Pr(>|z|) (Intercept) 4.1752 0.1787 23.36 <2e-16 *** x 2.9959 0.0475 63.07 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Correlation of Fixed Effects: (Intr) x -0.133 > VarCorr(ggl2) Groups Name Std.Dev. block (Intercept) 0.90348 > gP1 <- glmer(y ~ 1 + (1 | block), data = dP, family = poisson) > gP2 <- glmer(y ~ x + (1 | block), data = dP, family = poisson) > gG1 <- glmer(y ~ 1 + (1 | block), data = dG, family = gaussian(link = "log")) > gG2 <- glmer(y ~ x + (1 | block), data = dG, family = gaussian(link = "log")) > gGi1 <- glmer(y ~ 1 + (1 | block), data = dGi, family = gaussian(link = "inverse")) > gGi2 <- glmer(y ~ x + (1 | block), data = dGi, family = gaussian(link = "inverse")) ================================================================= ==547130==ERROR: AddressSanitizer: heap-use-after-free on address 0x7e3eb108c430 at pc 0x7b5e9c8ac93c bp 0x7fff740cc7f0 sp 0x7fff740cc7e8 READ of size 16 at 0x7e3eb108c430 thread T0 #0 0x7b5e9c8ac93b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7b5e9c8ac93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7b5e9c8ac93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7b5e9c8ac93b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7b5e9c8ac93b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7b5e9c8ac93b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7b5e9c8ac93b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7b5e9c8ac93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7b5e9c8ac93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7b5e9c8ac93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7b5e9c8ac93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7b5e9c8ac93b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7b5e9c83acd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7b5e9c83acd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7b5e9c839bc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x55708e2e3b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x55708e3a7d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x55708e3913be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x55708e38ed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x55708e3e7bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x55708e38e840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x55708e3e5269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x55708e38e840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x55708e3afeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x55708e3afeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x55708e39060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x55708e38e4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x55708e3909a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x55708e38e9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x55708e3e7bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x55708e38e840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x55708e3909a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x55708e38e9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x55708e3909a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x55708e38e9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x55708e39060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x55708e38e2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x55708e39c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x55708e3913be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x55708e38ed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x55708e3e5269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x55708e38e840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x55708e3afeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x55708e3afeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x55708e3913be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x55708e38ed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x55708e244abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x55708e39c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x55708e3913be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x55708e38ed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x55708e3e7bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x55708e38e840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x55708e3ecfba in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993:9 #75 0x55708e39c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #76 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #77 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #78 0x55708e39060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #79 0x55708e38e4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #80 0x55708e3ed883 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018:9 #81 0x55708e4964b9 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11 #82 0x55708e3a1f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #83 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #84 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #85 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #86 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #87 0x55708e3913be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #88 0x55708e38ed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #89 0x55708e38e840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #90 0x55708e45fbe1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #91 0x55708e462410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #92 0x55708e462410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #93 0x55708e4624a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #94 0x55708e163d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #95 0x7f5eb3f11574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #96 0x7f5eb3f11627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #97 0x55708e07b7d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7e3eb108c430 is located 48 bytes inside of 41648-byte region [0x7e3eb108c400,0x7e3eb10966b0) freed by thread T0 here: #0 0x55708e120916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x55708e47d31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x55708e47d31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x55708e47018b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x55708e46a99b in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2863:2 #5 0x55708e381ee1 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #6 0x55708e381ee1 in mkHandlerEntry /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:1659:18 #7 0x55708e381ee1 in R_withCallingErrorHandler /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:2600:18 #8 0x7f5eb0f054ff in R_evalHandleError /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:93:12 #9 0x7f5eb0f054ff in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1109:22 #10 0x55708e4a5853 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348:13 #11 0x55708e3aaa1f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085:12 #12 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #13 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #14 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #15 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #16 0x55708e3913be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #17 0x55708e4a6e97 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687:10 #18 0x55708e3cea0f in tryDispatch /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6090:16 #19 0x55708e39c1c2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8320:19 #20 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #21 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #22 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #23 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #24 0x55708e3913be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #25 0x55708e38ed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #26 0x55708e3e7bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #27 0x55708e38e840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #28 0x55708e3e5269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #29 0x55708e38e840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #30 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #31 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #32 0x55708e3afeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #33 0x55708e3afeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #34 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 previously allocated by thread T0 here: #0 0x55708e120bb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x55708e46ac7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x55708e1c332b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x55708e1c332b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7b5ea349c0ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x55708e2d8365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x55708e39c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x55708e3913be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x55708e49ce14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x55708e49ba98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x55708e49e073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x55708e3a1f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x55708e3913be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x55708e38ed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x55708e3ec653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x55708e39c77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x55708e38fd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x55708e38e301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x55708e3d6a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x55708e3d5c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x55708e3913be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x55708e38ed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x55708e3e7bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7e3eb108c180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e3eb108c200: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e3eb108c280: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e3eb108c300: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e3eb108c380: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7e3eb108c400: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7e3eb108c480: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e3eb108c500: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e3eb108c580: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e3eb108c600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e3eb108c680: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==547130==ABORTING Running the tests in ‘tests/glmmWeights.R’ failed. Complete output: > if (.Platform$OS.type != "windows") { + + library(lme4) + library(testthat) + + source(system.file("testdata/lme-tst-funs.R", package="lme4", mustWork=TRUE)) + ##-> gSim(), a general simulation function ... + + ## hand-coded Pearson residuals {for sumFun() } + mypresid <- function(x) { + mu <- fitted(x) + (getME(x,"y") - mu) * sqrt(weights(x)) / sqrt(x@resp$family$variance(mu)) + } + + ## should be equal (up to numerical error) to weights(.,type="working") + workingWeights <- function(mod) mod@resp$weights*(mod@resp$muEta()^2)/mod@resp$variance() + + ##' Sum of weighted residuals, 4 ways; the last three are identical + sumFun <- function(m) { + wrss1 <- m@devcomp$cmp["wrss"] + wrss2 <- sum(residuals(m,type="pearson")^2) + wrss3 <- sum(m@resp$wtres^2) + ## compare to hand-fitted Pearson resids ... + wrss4 <- sum(mypresid(m)^2) + c(wrss1,wrss2,wrss3,wrss4) + } + ## The relative "error"/differences of the weights w[] entries + rel.diff <- function(w) abs(1 - w[-1]/w[1]) + + set.seed(101) + + ## GAMMA + g0 <- glmer(y~x+(1|block),data=gSim(),family=Gamma) + expect_true(all(rel.diff(sumFun(g0)) < 1e-13)) + expect_equal(weights(g0, type = "working"), workingWeights(g0), + tolerance = 1e-4) ## FIXME: why is such a high tolerance required? + + ## BERNOULLI + g1 <- glmer(y~x+(1|block),data=gSim(family=binomial(),nbinom=1), + family=binomial) + expect_true(all(rel.diff(sumFun(g1)) < 1e-13)) + expect_equal(weights(g1, type = "working"), workingWeights(g1), + tolerance = 1e-5) ## FIXME: why is such a high tolerance required? + + + ## POISSON + (n <- nrow(d.P <- gSim(family=poisson()))) + g2 <- glmer(y ~ x + (1|block), data = d.P, family=poisson) + g2W <- glmer(y ~ x + (1|block), data = d.P, family=poisson, weights = rep(2,n)) + expect_true(all(rel.diff(sumFun(g2 )) < 1e-13)) + expect_true(all(rel.diff(sumFun(g2W)) < 1e-13)) + ## correct + expect_equal(weights(g2, type = "working"), workingWeights(g2), + tolerance = 1e-5) ## FIXME: why is such a high tolerance required? + expect_equal(weights(g2W, type = "working"), workingWeights(g2W), + tolerance = 1e-5) ## FIXME: why is such a high tolerance required? + + + ## non-Bernoulli BINOMIAL + g3 <- glmer(y ~ x + (1|block), data= gSim(family=binomial(), nbinom=10), + family=binomial) + expect_true(all(rel.diff(sumFun(g3)) < 1e-13)) + expect_equal(weights(g3, type = "working"), workingWeights(g3), + tolerance = 1e-4) ## FIXME: why is such a high tolerance required? + + + + d.b.2 <- gSim(nperblk = 2, family=binomial()) + g.b.2 <- glmer(y ~ x + (1|block), data=d.b.2, family=binomial) + + expect_true(all(rel.diff(sumFun(g.b.2 )) < 1e-13)) + + + ## Many blocks of only 2 observations each - (but nicely balanced) + ## Want this "as" https://github.com/lme4/lme4/issues/47 + ## (but it "FAILS" survival already): + ## + ## n2 = n/2 : + n2 <- 2048 + if(FALSE) + n2 <- 100 # for building/testing + set.seed(47) + dB2 <- gSim(n2, nperblk = 2, x= rep(0:1, each= n2), family=binomial()) + ## -- -- --- -------- + gB2 <- glmer(y ~ x + (1|block), data=dB2, family=binomial) + expect_true(all(rel.diff(sumFun(gB2)) < 1e-13)) + + ## NB: Finite sample bias of \hat\sigma_1 and \hat\beta_1 ("Intercept") + ## tend to zero only slowly for n2 -> Inf, e.g., for + ## n2 = 2048, b1 ~= 4.3 (instead of 4); s1 ~= 1.3 (instead of 1) + + ## FAILS ----- + ## library(survival) + ## (gSurv.B2 <- clogit(y ~ x + strata(block), data=dB2)) + ## ## --> Error in Surv(rep(1, 200L), y) : Time and status are different lengths + ## summary(gSurv.B2) + ## (SE.surf <- sqrt(diag(vcov(gSurv.B2)))) + + + + g3 <- glmer(y ~ x + (1|block),data=gSim(family=binomial(),nbinom=10), + family=binomial) + expect_equal(var(sumFun(g3)),0) + + ## check dispersion parameter + ## (lowered tolerance to pass checks on my machine -- SCW) + expect_equal(sigma(g0)^2, 0.4888248, tolerance=1e-4) + + } ## skip on windows (for speed) Loading required package: Matrix ================================================================= ==555415==ERROR: AddressSanitizer: heap-use-after-free on address 0x7ea16c5ac430 at pc 0x7bc157bc493c bp 0x7ffdf7b1e410 sp 0x7ffdf7b1e408 READ of size 16 at 0x7ea16c5ac430 thread T0 #0 0x7bc157bc493b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7bc157bc493b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7bc157bc493b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7bc157bc493b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7bc157bc493b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7bc157bc493b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7bc157bc493b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7bc157bc493b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7bc157bc493b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7bc157bc493b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7bc157bc493b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7bc157bc493b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7bc157b52cd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7bc157b52cd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7bc157b51bc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x55bfce7d0b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x55bfce894d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x55bfce87cd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x55bfce87b301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x55bfce87e3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x55bfce87bd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x55bfce8d4bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x55bfce87b840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x55bfce8d2269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x55bfce87b840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x55bfce89ceba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x55bfce89ceba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x55bfce87cd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x55bfce87b301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x55bfce87d60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x55bfce87b4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x55bfce87d9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x55bfce87b9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x55bfce8d4bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x55bfce87b840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x55bfce87d9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x55bfce87b9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x55bfce87d9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x55bfce87b9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x55bfce87d60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x55bfce87b2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x55bfce88977a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x55bfce87cd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x55bfce87b301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x55bfce87e3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x55bfce87bd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x55bfce8d2269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x55bfce87b840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x55bfce89ceba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x55bfce89ceba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x55bfce87cd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x55bfce87b301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x55bfce87e3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x55bfce87bd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x55bfce731abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x55bfce88977a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x55bfce87cd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x55bfce87b301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x55bfce87e3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x55bfce87bd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x55bfce8d4bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x55bfce87b840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x55bfce8d2269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #75 0x55bfce87b840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #76 0x55bfce87b840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #77 0x55bfce94cbe1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #78 0x55bfce94f410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #79 0x55bfce94f410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #80 0x55bfce94f4a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #81 0x55bfce650d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #82 0x7fc16f212574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x7fc16f212627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #84 0x55bfce5687d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7ea16c5ac430 is located 48 bytes inside of 41648-byte region [0x7ea16c5ac400,0x7ea16c5b66b0) freed by thread T0 here: #0 0x55bfce60d916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x55bfce96a31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x55bfce96a31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x55bfce95d18b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x55bfce95a195 in Rf_cons /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2488:2 #5 0x55bfce830b7b in Rf_defineVar /data/gannet/ripley/R/svn/R-devel/src/main/envir.c:1996:21 #6 0x55bfce8cd50e in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2550:5 #7 0x7fc16ccbdf40 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154:19 #8 0x55bfce992853 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348:13 #9 0x55bfce897a1f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085:12 #10 0x55bfce87cd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #11 0x55bfce87b301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #12 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #13 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #14 0x55bfce87e3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #15 0x55bfce993e97 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687:10 #16 0x55bfce8dbd49 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4191:14 #17 0x55bfceaafa0a in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:671:16 #18 0x55bfceabcb2f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264:8 #19 0x55bfce87b840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #20 0x55bfce87b541 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1219:19 #21 0x55bfce8d2269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #22 0x55bfce87b840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #23 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #24 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #25 0x55bfce89ceba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #26 0x55bfce89ceba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #27 0x55bfce87cd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #28 0x55bfce87b301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #29 0x55bfce87d60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #30 0x55bfce87b4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #31 0x55bfce87d9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 previously allocated by thread T0 here: #0 0x55bfce60dbb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x55bfce957c7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x55bfce6b032b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x55bfce6b032b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7bc15e6d80ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x55bfce7c5365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x55bfce88977a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x55bfce87cd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x55bfce87b301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x55bfce87e3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x55bfce989e14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x55bfce988a98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x55bfce98b073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x55bfce88ef93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x55bfce87cd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x55bfce87b301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x55bfce87e3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x55bfce87bd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x55bfce8d9653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x55bfce88977a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x55bfce87cd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x55bfce87b301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x55bfce8c3a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x55bfce8c2c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x55bfce87e3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x55bfce87bd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x55bfce8d4bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7ea16c5ac180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7ea16c5ac200: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7ea16c5ac280: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7ea16c5ac300: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7ea16c5ac380: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7ea16c5ac400: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7ea16c5ac480: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ea16c5ac500: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ea16c5ac580: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ea16c5ac600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7ea16c5ac680: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==555415==ABORTING Running the tests in ‘tests/optimizer.R’ failed. Complete output: > library(lme4) Loading required package: Matrix > source(system.file("test-tools-1.R", package = "Matrix"), keep.source = FALSE) Loading required package: tools > ## N.B. is.all.equal4() and assert.EQ() use 'tol', not 'tolerance' > > > ## should be able to run any example with any bounds-constrained optimizer ... > ## Nelder_Mead, bobyqa built in; optimx/nlminb, optimx/L-BFGS-B > ## optimx/Rcgmin will require a bit more wrapping/interface work (requires gradient) > > if (.Platform$OS.type != "windows") { + fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) ## Nelder_Mead + fm1B <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, + control=lmerControl(optimizer="bobyqa")) + stopifnot(all.equal(fixef(fm1),fixef(fm1B))) + require(optimx) + lmerCtrl.optx <- function(method, ...) + lmerControl(optimizer="optimx", ..., optCtrl=list(method=method)) + glmerCtrl.optx <- function(method, ...) + glmerControl(optimizer="optimx", ..., optCtrl=list(method=method)) + + (testLevel <- lme4:::testLevel()) + + ## FAILS on Windows (on r-forge only, not win-builder)... 'function is infeasible at initial parameters' + ## (can we test whether we are on r-forge??) + if (.Platform$OS.type != "windows") { + fm1C <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, + control=lmerCtrl.optx(method="nlminb")) + fm1D <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, + control=lmerCtrl.optx(method="L-BFGS-B")) + stopifnot(is.all.equal4(fixef(fm1),fixef(fm1B),fixef(fm1C),fixef(fm1D))) + + fm1E <- update(fm1,control=lmerCtrl.optx(method=c("nlminb","L-BFGS-B"))) + ## hack equivalence of call and optinfo + fm1E@call <- fm1C@call + fm1E@optinfo <- fm1C@optinfo + assert.EQ(fm1C,fm1E, tol=1e-5, giveRE=TRUE)# prints unless tolerance=0--equality + } + + gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), + data = cbpp, family = binomial, + control=glmerControl(tolPwrss=1e-13)) + gm1B <- update(gm1, control=glmerControl (tolPwrss=1e-13, optimizer="bobyqa")) + gm1C <- update(gm1, control=glmerCtrl.optx(tolPwrss=1e-13, method="nlminb")) + gm1D <- update(gm1, control=glmerCtrl.optx(tolPwrss=1e-13, method="L-BFGS-B")) + stopifnot(is.all.equal4(fixef(gm1),fixef(gm1B),fixef(gm1C),fixef(gm1D), + tol=1e-5)) + + if (testLevel > 1) { + gm1E <- update(gm1, control= + glmerCtrl.optx(tolPwrss=1e-13, method=c("nlminb","L-BFGS-B"))) + ## hack equivalence of call and optinfo + gm1E@call <- gm1C@call + gm1E@optinfo <- gm1C@optinfo + assert.EQ(gm1E,gm1C, tol=1e-5, giveRE=TRUE)# prints unless tol=0--equality + } + } ## skip on windows (for speed) Loading required package: optimx ================================================================= ==590431==ERROR: AddressSanitizer: heap-use-after-free on address 0x7cccbe7cd0b0 at pc 0x7b0caa64b93c bp 0x7ffd16119cd0 sp 0x7ffd16119cc8 READ of size 16 at 0x7cccbe7cd0b0 thread T0 #0 0x7b0caa64b93b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7b0caa64b93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7b0caa64b93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7b0caa64b93b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7b0caa64b93b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7b0caa64b93b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7b0caa64b93b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7b0caa64b93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7b0caa64b93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7b0caa64b93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7b0caa64b93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7b0caa64b93b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7b0caa5d9cd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7b0caa5d9cd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7b0caa5d8bc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x562662595b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x562662659d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x562662640d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x562662699bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x562662640840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x562662697269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x562662640840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x562662661eba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x562662661eba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #34 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #35 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #36 0x562662640d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #37 0x7b0cb1255ad9 in port_nlminb /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/port.c:420:18 #38 0x562662595e39 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #39 0x56266259e8d5 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11 #40 0x56266264e77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #41 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #42 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #43 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #44 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #45 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #46 0x562662640d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #47 0x5626624f6abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #48 0x56266264e77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #49 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #50 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #51 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #52 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #53 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #54 0x562662640d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #55 0x56266269e653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #56 0x56266264e77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #57 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #58 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #59 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #60 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #61 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #62 0x56266274ee14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #63 0x56266274d8b8 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:509:10 #64 0x562662750073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #65 0x562662653f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #66 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x56266269260a in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567:11 #70 0x7f0cbf6d4f40 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154:19 #71 0x562662757853 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348:13 #72 0x562662640d7d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1262:9 #73 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #74 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #75 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #76 0x562662640d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #77 0x562662699bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #78 0x562662640840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #79 0x562662697269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #80 0x562662640840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #81 0x562662640840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #82 0x562662711be1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #83 0x562662714410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #84 0x562662714410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #85 0x5626627144a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #86 0x562662415d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #87 0x7f0cc1c12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #88 0x7f0cc1c12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #89 0x56266232d7d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7cccbe7cd0b0 is located 48 bytes inside of 1840-byte region [0x7cccbe7cd080,0x7cccbe7cd7b0) freed by thread T0 here: #0 0x5626623d2916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x56266272f31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x56266272f31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x56266272218b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x562662720ef9 in R_gc /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3091:5 #5 0x562662720ef9 in do_gc /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2131:2 #6 0x56266264e77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x562662640d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #13 0x5626624f6abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #14 0x56266264e77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #15 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #16 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #17 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #18 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #19 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #20 0x562662640d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #21 0x56266269e653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #22 0x56266264e77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #23 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #24 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #25 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #26 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #27 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #28 0x56266274ee14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #29 0x56266274d8b8 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:509:10 #30 0x562662750073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #31 0x562662653f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 previously allocated by thread T0 here: #0 0x5626623d2bb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x56266271cc7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x56266247532b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x56266247532b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7b0cb129c0ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x56266258a365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x56266264e77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x56266274ee14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x56266274da98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x562662750073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x562662653f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x562662640d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x56266269e653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x56266264e77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x562662641d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x562662640301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x562662688a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x562662687c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x5626626433be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x562662640d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x56266269e653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7cccbe7cce00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cccbe7cce80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cccbe7ccf00: fd fd fd fd fd fd fd fd fd fd fd fa fa fa fa fa 0x7cccbe7ccf80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7cccbe7cd000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7cccbe7cd080: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7cccbe7cd100: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cccbe7cd180: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cccbe7cd200: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cccbe7cd280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cccbe7cd300: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==590431==ABORTING Running the tests in ‘tests/respiratory.R’ failed. Complete output: > ## Data originally from Davis 1991 Stat. Med., as packaged in geepack > ## and transformed (center, id -> factor, idctr created, levels labeled) > library(lme4) Loading required package: Matrix > > if (.Platform$OS.type != "windows") { + load(system.file("testdata","respiratory.RData",package="lme4")) + m_glmer_4.L <- glmer(outcome~center+treat+sex+age+baseline+(1|idctr), + family=binomial,data=respiratory) + + m_glmer_4.GHQ5 <- glmer(outcome~center+treat+sex+age+baseline+(1|idctr), + family=binomial,data=respiratory,nAGQ=5) + + m_glmer_4.GHQ8 <- glmer(outcome~center+treat+sex+age+baseline+(1|idctr), + family=binomial,data=respiratory,nAGQ=8) + + m_glmer_4.GHQ16 <- glmer(outcome~center+treat+sex+age+baseline+(1|idctr), + family=binomial,data=respiratory,nAGQ=16) + } ## skip on windows (for speed) ================================================================= ==616278==ERROR: AddressSanitizer: heap-use-after-free on address 0x7dc7bf812230 at pc 0x7b27ab4de93c bp 0x7fff58094c90 sp 0x7fff58094c88 READ of size 16 at 0x7dc7bf812230 thread T0 #0 0x7b27ab4de93b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7b27ab4de93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7b27ab4de93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7b27ab4de93b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7b27ab4de93b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7b27ab4de93b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7b27ab4de93b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7b27ab4de93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7b27ab4de93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7b27ab4de93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7b27ab4de93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7b27ab4de93b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7b27ab46ccd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7b27ab46ccd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7b27ab46bbc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x55b911ac9b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x55b911b8dd2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x55b911b75d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x55b911b74301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x55b911bbbc58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x55b911b773be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x55b911b74d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x55b911bcdbc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x55b911b74840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x55b911bcb269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x55b911b74840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x55b911bbbc58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x55b911b95eba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x55b911b95eba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x55b911b75d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x55b911b74301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x55b911b7660a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x55b911b744f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x55b911b769a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x55b911b749d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x55b911bcdbc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x55b911b74840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x55b911b769a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x55b911b749d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x55b911b769a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x55b911b749d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x55b911b7660a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x55b911b742b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x55b911b8277a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x55b911b75d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x55b911b74301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x55b911bbbc58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x55b911b773be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x55b911b74d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x55b911bcb269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x55b911b74840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x55b911bbbc58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x55b911b95eba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x55b911b95eba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x55b911b75d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x55b911b74301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x55b911bbbc58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x55b911b773be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x55b911b74d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x55b911a2aabc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x55b911b8277a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x55b911b75d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x55b911b74301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x55b911bbbc58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x55b911b773be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x55b911b74d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x55b911bcdbc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x55b911b74840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x55b911bcb269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #75 0x55b911b74840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #76 0x55b911b74840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #77 0x55b911c45be1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #78 0x55b911c48410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #79 0x55b911c48410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #80 0x55b911c484a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #81 0x55b911949d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #82 0x7f27c2b11574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x7f27c2b11627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #84 0x55b9118617d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7dc7bf812230 is located 48 bytes inside of 21360-byte region [0x7dc7bf812200,0x7dc7bf817570) freed by thread T0 here: #0 0x55b911906916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x55b911c6331b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x55b911c6331b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x55b911c5618b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x55b911c6bfc5 in CONS_NR /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2519:2 #5 0x55b911c4d22a in Rf_matchArgs_NR /data/gannet/ripley/R/svn/R-devel/src/main/match.c:196:12 #6 0x55b911c4ec58 in Rf_matchArgs_RC /data/gannet/ripley/R/svn/R-devel/src/main/match.c:392:17 #7 0x55b911bbbfa6 in make_applyClosure_env /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2261:15 #8 0x55b911bbbb25 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2304:19 #9 0x55b911b773be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #10 0x55b911b74d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #11 0x55b911bc69cb in do_if /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2709:20 #12 0x55b911b74840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #13 0x55b911bcb269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #14 0x55b911b74840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #15 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #16 0x55b911bc660a in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567:11 #17 0x7f27bf9e9f40 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154:19 #18 0x55b911c8b853 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348:13 #19 0x55b911b90a1f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085:12 #20 0x55b911b75d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #21 0x55b911b74301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #22 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #23 0x55b911bbbc58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #24 0x55b911b773be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #25 0x55b911c8ce97 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687:10 #26 0x55b911bb4a0f in tryDispatch /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6090:16 #27 0x55b911b821c2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8320:19 #28 0x55b911b75d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #29 0x55b911b74301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #30 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 previously allocated by thread T0 here: #0 0x55b911906bb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x55b911c50c7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x55b9119a932b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x55b9119a932b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7b27b209c0ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x55b911abe365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x55b911b8277a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x55b911b75d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x55b911b74301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x55b911bbbc58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x55b911b773be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x55b911c82e14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x55b911c81a98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x55b911c84073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x55b911b87f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x55b911b75d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x55b911b74301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x55b911bbbc58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x55b911b773be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x55b911b74d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x55b911bd2653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x55b911b8277a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x55b911b75d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x55b911b74301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x55b911bbca9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x55b911bbbc58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x55b911b773be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x55b911b74d28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x55b911bcdbc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7dc7bf811f80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dc7bf812000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dc7bf812080: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dc7bf812100: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dc7bf812180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7dc7bf812200: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7dc7bf812280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7dc7bf812300: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7dc7bf812380: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7dc7bf812400: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7dc7bf812480: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==616278==ABORTING Running the tests in ‘tests/testcrab.R’ failed. Complete output: > library("lme4") Loading required package: Matrix > L <- load(system.file("testdata","crabs_randdata2.Rda",package="lme4")) > ## randdata0: simulated data, in form suitable for plotting > ## randdata: simulated data, in form suitable for analysis > > ## fr ## alive/dead formula > ## fr2 ## proportion alive formula (use with weights=initial.snail.density) > > ## FIXME: there are still bigger differences than I'd like between the approaches > ## (mostly in the random-effects correlation). It's not clear who's right; > ## lme4 thinks its parameters are better, but ?? Could be explored further. > > if (FALSE) { + ## library(ggplot2) ## commented to avoid triggering Suggests: requirement + library(grid) + zmargin <- theme(panel.margin=unit(0,"lines")) + theme_set(theme_bw()) + g1 <- ggplot(randdata0,aes(x=snail.size,y=surv,colour=snail.size,fill=snail.size))+ + geom_hline(yintercept=1,colour="black")+ + stat_sum(aes(size=factor(..n..)),alpha=0.6)+ + facet_grid(.~ttt)+zmargin+ + geom_boxplot(fill=NA,outlier.colour=NULL,outlier.shape=3)+ ## set outliers to same colour as points + ## (hard to see which are outliers, but it doesn't really matter in this case) + scale_size_discrete("# obs",range=c(2,5)) + } > > if (.Platform$OS.type != "windows") { + t1 <- system.time(glmer1 <- glmer(fr2,weights=initial.snail.density, + family ="binomial", data=randdata)) + t1B <- system.time(glmer1B <- glmer(fr,family ="binomial", data=randdata)) + + res1 <- c(fixef(glmer1),c(VarCorr(glmer1)$plot)) + res1B <- c(fixef(glmer1B),c(VarCorr(glmer1B)$plot)) + p1 <- unlist(getME(glmer1,c("theta","beta"))) + stopifnot(all.equal(res1,res1B)) + + dfun <- update(glmer1,devFunOnly=TRUE) + stopifnot(all.equal(dfun(p1),c(-2*logLik(glmer1)))) + ## + ## library(lme4.0) ## version 0.999999.2 results + ## t1_lme4.0 <- system.time(glmer1X <- + ## glmer(fr2,weights=initial.snail.density, + ## family ="binomial", data=randdata)) + ## dput(c(fixef(glmer1X),c(VarCorr(glmer1X)$plot))) + ## p1X <- c(getME(glmer1X,"theta"),getME(glmer1X,"beta")) + p1X <- c(0.681301656652347, -1.14775239687404, 0.436143018123226, + 2.77730476938968, 0.609023583738824, -1.60055813739844, 2.0324468778545, + 0.624173873057839, -1.7908793509579, -2.44540201631615, -1.42365990002708, + -2.26780929006268, 0.700928084600075, -1.26220238391029, 0.369024582097804, + 3.44325347343035, 2.26400391093108) + stopifnot(all.equal(unname(p1),p1X,tolerance=0.03)) + dfun(p1X) + dfun(p1) + ## ~ 1.8 seconds elapsed time + lme4.0_res <- + structure(c(2.77730476938968, 0.609023583738824, -1.60055813739844, + 2.0324468778545, 0.624173873057839, -1.7908793509579, -2.44540201631615, + -1.42365990002708, -2.26780929006268, 0.700928084600075, -1.26220238391029, + 0.369024582097804, 3.44325347343035, 2.26400391093108, 0.464171947357232, + -0.532754465140956, -0.532754465140956, 0.801690946568518), + .Names = c("(Intercept)", + "crab.speciesS", "crab.speciesW", "crab.sizeS", "crab.sizeM", + "snail.sizeS", "crab.speciesS:crab.sizeS", "crab.speciesS:crab.sizeM", + "crab.speciesS:snail.sizeS", "crab.speciesW:snail.sizeS", + "crab.sizeS:snail.sizeS", "crab.sizeM:snail.sizeS", + "crab.speciesS:crab.sizeS:snail.sizeS", + "crab.speciesS:crab.sizeM:snail.sizeS", "", "", "", "")) + + stopifnot(all.equal(res1,lme4.0_res,tolerance=0.015)) + + + ## library("glmmADMB") + ## prop/weights formulation: ~ 7 seconds + ## t1_glmmadmb <- system.time(glmer1B <- glmmadmb(fr,family ="binomial", + ## corStruct="full",data=randdata)) + ## dput(c(fixef(glmer1B),c(VarCorr(glmer1B)$plot))) + glmmADMB_res <- structure(c(2.7773101267224, 0.609026276823218, -1.60055704634712, + 2.03244174458562, 0.624171008585953, -1.79088398816641, -2.44540300134182, + -1.42366043619683, -2.26780858382505, 0.700927141726545, -1.26219964572264, + 0.369029052442189, 3.44326297908383, 2.26403738918967, 0.46417, + -0.53253, -0.53253, 0.80169), .Names = c("(Intercept)", "crab.speciesS", + "crab.speciesW", "crab.sizeS", "crab.sizeM", "snail.sizeS", "crab.speciesS:crab.sizeS", + "crab.speciesS:crab.sizeM", "crab.speciesS:snail.sizeS", "crab.speciesW:snail.sizeS", + "crab.sizeS:snail.sizeS", "crab.sizeM:snail.sizeS", "crab.speciesS:crab.sizeS:snail.sizeS", + "crab.speciesS:crab.sizeM:snail.sizeS", "", "", "", "")) + + stopifnot(all.equal(res1B,glmmADMB_res,tolerance=0.015)) + } ## skip on windows (for speed) ================================================================= ==627080==ERROR: AddressSanitizer: heap-use-after-free on address 0x7d7976e40130 at pc 0x7b3962d1593c bp 0x7ffdb38f8250 sp 0x7ffdb38f8248 READ of size 16 at 0x7d7976e40130 thread T0 #0 0x7b3962d1593b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7b3962d1593b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7b3962d1593b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7b3962d1593b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7b3962d1593b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7b3962d1593b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7b3962d1593b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7b3962d1593b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7b3962d1593b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7b3962d1593b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7b3962d1593b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7b3962d1593b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7b3962ca3cd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7b3962ca3cd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7b3962ca2bc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x556936e13b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x556936ed7d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x556936ebed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x556936f17bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x556936ebe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x556936f15269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x556936ebe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x556936edfeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x556936edfeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x556936ec060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x556936ebe4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x556936ec09a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x556936ebe9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x556936f17bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x556936ebe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x556936ec09a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x556936ebe9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x556936ec09a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x556936ebe9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x556936ec060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x556936ebe2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x556936ecc77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x556936ebed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x556936f15269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x556936ebe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x556936edfeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x556936edfeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x556936ebed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x556936d74abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x556936ecc77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x556936ebed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x556936f17bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x556936ebe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x556936ec060a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #75 0x556936eeb1b1 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5867:6 #76 0x556936eeb1b1 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7880:20 #77 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #78 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #79 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #80 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #81 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #82 0x556936ebed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #83 0x556936f17bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #84 0x556936ebe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #85 0x556936f15269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #86 0x556936ebe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #87 0x556936ebe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #88 0x556936f8fbe1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #89 0x556936f92410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #90 0x556936f92410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #91 0x556936f924a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #92 0x556936c93d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #93 0x7f397a311574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #94 0x7f397a311627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #95 0x556936bab7d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7d7976e40130 is located 48 bytes inside of 7664-byte region [0x7d7976e40100,0x7d7976e41ef0) freed by thread T0 here: #0 0x556936c50916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x556936fad31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x556936fad31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x556936fa018b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x556936fb70e5 in Rf_mkPROMISE /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2613:2 #5 0x556936f06136 in make_applyClosure_env /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2280:16 #6 0x556936f05b25 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2304:19 #7 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #8 0x556936ebed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #9 0x556936f109cb in do_if /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2709:20 #10 0x556936ebe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #11 0x556936f15269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #12 0x556936ebe840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #13 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #14 0x556936f1060a in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567:11 #15 0x7f3977335f40 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154:19 #16 0x556936fd5853 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348:13 #17 0x556936edaa1f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085:12 #18 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #19 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #20 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #21 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #22 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #23 0x556936fd6e97 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687:10 #24 0x556936efea0f in tryDispatch /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6090:16 #25 0x556936ecc1c2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8320:19 #26 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #27 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #28 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #29 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #30 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 previously allocated by thread T0 here: #0 0x556936c50bb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x556936f9ac7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x556936cf332b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x556936cf332b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7b396989c0ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x556936e08365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x556936ecc77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x556936fcce14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x556936fcba98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x556936fce073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x556936ed1f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x556936ebed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x556936f1c653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x556936ecc77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x556936ebfd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x556936ebe301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x556936f06a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x556936f05c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x556936ec13be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x556936ebed28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x556936f17bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7d7976e3fe80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d7976e3ff00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d7976e3ff80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d7976e40000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d7976e40080: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d7976e40100: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7d7976e40180: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7976e40200: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7976e40280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7976e40300: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d7976e40380: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==627080==ABORTING Running the tests in ‘tests/throw.R’ failed. Complete output: > ## original code was designed to detect segfaults/hangs from error handling > > library(lme4) Loading required package: Matrix > set.seed(101) > d <- expand.grid(block = LETTERS[1:26], + rep = 1:100) > d$x <- runif(nrow(d)) > reff_f <- rnorm(length(levels(d$block)),sd=1) > ## need intercept large enough to avoid negative values > d$eta0 <- 4+3*d$x ## version without random effects > d$eta <- d$eta0+reff_f[d$block] > ## inverse link > d$mu <- 1/d$eta > d$y <- rgamma(nrow(d), scale=d$mu/2, shape=2) > > if (.Platform$OS.type != "windows") { + gm0 <- glmer(y ~ 1|block, d, Gamma) + gm0.A25 <- glmer(y ~ 1|block, d, Gamma, nAGQ=25L) + gm1 <- glmer(y ~ x + (1|block), d, Gamma) + gm1.A25 <- glmer(y ~ x + (1|block), d, Gamma, nAGQ=25L) + + ## strange things happening for logLik ==> AIC, etc for nAGQ ??? + anova(gm0, gm1) + anova(gm0, gm0.A25) + anova(gm1, gm1.A25) + + summary(gm1) # "fine" + summary(gm1.A25) # Inf logLik etc ? + + } ================================================================= ==631261==ERROR: AddressSanitizer: heap-use-after-free on address 0x7e80b8d94430 at pc 0x7ba0a4b5e93c bp 0x7ffe0c4056d0 sp 0x7ffe0c4056c8 READ of size 16 at 0x7e80b8d94430 thread T0 #0 0x7ba0a4b5e93b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7ba0a4b5e93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7ba0a4b5e93b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7ba0a4b5e93b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7ba0a4b5e93b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7ba0a4b5e93b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7ba0a4b5e93b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7ba0a4b5e93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7ba0a4b5e93b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7ba0a4b5e93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7ba0a4b5e93b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7ba0a4b5e93b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7ba0a4aeccd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7ba0a4aeccd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7ba0a4aebbc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x56139be62b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x56139bf26d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x56139bf0ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x56139bf0d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x56139bf55a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x56139bf54c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x56139bf103be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x56139bf0dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x56139bf66bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x56139bf0d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x56139bf64269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x56139bf0d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x56139bf55a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x56139bf54c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x56139bf2eeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x56139bf2eeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x56139bf0ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x56139bf0d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x56139bf0f60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x56139bf0d4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x56139bf0f9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x56139bf0d9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x56139bf66bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x56139bf0d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x56139bf0f9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x56139bf0d9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x56139bf0f9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x56139bf0d9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x56139bf0f60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x56139bf0d2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x56139bf1b77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x56139bf0ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x56139bf0d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x56139bf55a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x56139bf54c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x56139bf103be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x56139bf0dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x56139bf64269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x56139bf0d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x56139bf55a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x56139bf54c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x56139bf2eeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x56139bf2eeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x56139bf0ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x56139bf0d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x56139bf55a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x56139bf54c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x56139bf103be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x56139bf0dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x56139bdc3abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x56139bf1b77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x56139bf0ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x56139bf0d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x56139bf55a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x56139bf54c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x56139bf103be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x56139bf0dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x56139bf66bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x56139bf0d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x56139bf64269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #75 0x56139bf0d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #76 0x56139bf0d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #77 0x56139bfdebe1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #78 0x56139bfe1410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #79 0x56139bfe1410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #80 0x56139bfe14a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #81 0x56139bce2d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #82 0x7fa0bc111574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x7fa0bc111627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #84 0x56139bbfa7d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7e80b8d94430 is located 48 bytes inside of 41648-byte region [0x7e80b8d94400,0x7e80b8d9e6b0) freed by thread T0 here: #0 0x56139bc9f916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x56139bffc31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x56139bffc31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x56139bfef18b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x56139c0060e5 in Rf_mkPROMISE /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2613:2 #5 0x56139c006a87 in R_mkEVPROMISE_NR /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2653:17 #6 0x56139c141905 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:666:9 #7 0x56139c14eb2f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264:8 #8 0x56139bf0d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #9 0x56139bf0d541 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1219:19 #10 0x56139bf64269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #11 0x56139bf0d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #12 0x56139bf55a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #13 0x56139bf54c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #14 0x56139bf2eeba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #15 0x56139bf2eeba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #16 0x56139bf0ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x56139bf0d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x56139bf0f60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #19 0x56139bf0d4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #20 0x56139bf0f9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #21 0x56139bf0d9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #22 0x56139bf66bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #23 0x56139bf0d840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #24 0x56139bf0f9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #25 0x56139bf0d9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #26 0x56139bf0f9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #27 0x56139bf0d9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #28 0x56139bf0f60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #29 0x56139bf0d2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #30 0x56139bf1b77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #31 0x56139bf0ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 previously allocated by thread T0 here: #0 0x56139bc9fbb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x56139bfe9c7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x56139bd4232b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x56139bd4232b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7ba0ab69c0ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x56139be57365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x56139bf1b77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x56139bf0ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x56139bf0d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x56139bf55a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x56139bf54c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x56139bf103be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x56139c01be14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x56139c01aa98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x56139c01d073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x56139bf20f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x56139bf0ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x56139bf0d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x56139bf55a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x56139bf54c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x56139bf103be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x56139bf0dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x56139bf6b653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x56139bf1b77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x56139bf0ed74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x56139bf0d301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x56139bf55a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x56139bf54c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x56139bf103be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x56139bf0dd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x56139bf66bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7e80b8d94180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e80b8d94200: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e80b8d94280: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e80b8d94300: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e80b8d94380: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7e80b8d94400: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7e80b8d94480: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e80b8d94500: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e80b8d94580: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e80b8d94600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e80b8d94680: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==631261==ABORTING Running the tests in ‘tests/varcorr.R’ failed. Complete output: > library(lme4) Loading required package: Matrix > > if (.Platform$OS.type != "windows") { + data(Orthodont, package="nlme") + fm1 <- lmer(distance ~ age + (age|Subject), data = Orthodont) + VarCorr(fm1) + + fm2ML <- lmer(diameter ~ 1 + (1|plate) + (1|sample), Penicillin, REML=0) + VarCorr(fm2ML) + + gm1 <- glmer(cbind(incidence,size-incidence) ~ period + (1|herd),data=cbpp, + family=binomial) + VarCorr(gm1) + + cbpp$obs <- factor(seq(nrow(cbpp))) + gm2 <- update(gm1,.~.+(1|obs)) + VarCorr(gm2) + + if (FALSE) { + ## testing lme4/lme4 incompatibility + ## library(lme4) + VarCorr(fm1) + lme4:::VarCorr.merMod(fm1) ## OK + } + } ## skip on windows (for speed) ================================================================= ==636957==ERROR: AddressSanitizer: heap-use-after-free on address 0x7cd1883a80b0 at pc 0x7b117411593c bp 0x7ffdad40be70 sp 0x7ffdad40be68 READ of size 16 at 0x7cd1883a80b0 thread T0 #0 0x7b117411593b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7b117411593b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7b117411593b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7b117411593b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7b117411593b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7b117411593b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7b117411593b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7b117411593b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7b117411593b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7b117411593b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7b117411593b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7b117411593b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7b11740a3cd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7b11740a3cd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7b11740a2bc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x55b761624b06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x55b7616e8d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x55b7616d0d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x55b7616cf301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x55b761717a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x55b761716c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x55b7616d23be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x55b7616cfd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x55b761728bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x55b7616cf840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x55b761726269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x55b7616cf840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x55b761717a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x55b761716c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x55b7616f0eba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x55b7616f0eba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x55b7616d0d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x55b7616cf301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x55b761717a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #34 0x55b761716c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #35 0x55b7616d23be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #36 0x55b7616cfd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #37 0x55b761728bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x55b7616cf840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x55b761726269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #40 0x55b7616cf840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #41 0x55b7616cf840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #42 0x55b7617a0be1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #43 0x55b7617a3410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #44 0x55b7617a3410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #45 0x55b7617a34a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #46 0x55b7614a4d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #47 0x7f118b711574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #48 0x7f118b711627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #49 0x55b7613bc7d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7cd1883a80b0 is located 48 bytes inside of 1840-byte region [0x7cd1883a8080,0x7cd1883a87b0) freed by thread T0 here: #0 0x55b761461916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x55b7617be31b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x55b7617be31b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x55b7617b118b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x55b7617ae195 in Rf_cons /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2488:2 #5 0x55b7617161b3 in promiseArgsEx /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3789:26 #6 0x55b76172fc4e in Rf_promiseArgs /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3854:12 #7 0x55b76172fc4e in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4186:14 #8 0x55b761903a0a in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:671:16 #9 0x55b761910b2f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264:8 #10 0x55b7616cf840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #11 0x55b7616cf541 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1219:19 #12 0x55b761726269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #13 0x55b7616cf840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #14 0x55b761717a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #15 0x55b761716c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #16 0x55b7616f0eba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #17 0x55b7616f0eba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #18 0x55b7616d0d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #19 0x55b7616cf301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #20 0x55b761717a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #21 0x55b761716c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #22 0x55b7616d23be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #23 0x55b7616cfd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #24 0x55b761728bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #25 0x55b7616cf840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #26 0x55b761726269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #27 0x55b7616cf840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #28 0x55b7616cf840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #29 0x55b7617a0be1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #30 0x55b7617a3410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #31 0x55b7617a3410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #32 0x55b7617a34a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #33 0x55b7614a4d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 previously allocated by thread T0 here: #0 0x55b761461bb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x55b7617abc7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x55b76150432b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x55b76150432b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7b117ac9c0ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x55b761619365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x55b7616dd77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x55b7616d0d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x55b7616cf301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x55b761717a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x55b761716c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x55b7616d23be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x55b7617dde14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x55b7617dca98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x55b7617df073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x55b7616e2f93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x55b7616d0d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x55b7616cf301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x55b761717a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x55b761716c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x55b7616d23be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x55b7616cfd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x55b76172d653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x55b7616dd77a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x55b7616d0d74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x55b7616cf301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x55b761717a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x55b761716c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x55b7616d23be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x55b7616cfd28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x55b761728bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7cd1883a7e00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd1883a7e80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd1883a7f00: fd fd fd fd fd fd fd fd fd fd fd fa fa fa fa fa 0x7cd1883a7f80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7cd1883a8000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7cd1883a8080: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7cd1883a8100: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd1883a8180: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd1883a8200: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd1883a8280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd1883a8300: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==636957==ABORTING * checking package vignettes ... OK * checking re-building of vignette outputs ... [18m/42m] ERROR Error(s) in re-building vignettes: --- re-building ‘autoscale.Rmd’ using rmarkdown --- finished re-building ‘autoscale.Rmd’ --- re-building ‘covariance_structures.Rmd’ using rmarkdown ================================================================= ==653434==ERROR: AddressSanitizer: heap-use-after-free on address 0x7d6a90a1d530 at pc 0x7b3a7b0b193c bp 0x7ffe7268f6d0 sp 0x7ffe7268f6c8 READ of size 16 at 0x7d6a90a1d530 thread T0 #0 0x7b3a7b0b193b in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 #1 0x7b3a7b0b193b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeff(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:58 #2 0x7b3a7b0b193b in Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>::assignCoeffByOuterInner(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668:5 #3 0x7b3a7b0b193b in Eigen::internal::dense_assignment_loop, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>, 0, 0>::run(Eigen::internal::generic_dense_assignment_kernel, 0, Eigen::Stride<0, 0>>>, Eigen::internal::evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>, Eigen::internal::assign_op, 0>&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347:16 #4 0x7b3a7b0b193b in void Eigen::internal::call_dense_assignment_loop, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #5 0x7b3a7b0b193b in Eigen::internal::Assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #6 0x7b3a7b0b193b in void Eigen::internal::call_assignment_no_alias, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #7 0x7b3a7b0b193b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, Eigen::internal::assign_op>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>::value, void*>::type) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #8 0x7b3a7b0b193b in void Eigen::internal::call_assignment, 0, Eigen::Stride<0, 0>>, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::Map, 0, Eigen::Stride<0, 0>>&, Eigen::Product, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #9 0x7b3a7b0b193b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::MatrixBase, 0, Eigen::Stride<0, 0>>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #10 0x7b3a7b0b193b in Eigen::Map, 0, Eigen::Stride<0, 0>>& Eigen::Map, 0, Eigen::Stride<0, 0>>::operator=, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>>(Eigen::DenseBase, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Map.h:162:5 #11 0x7b3a7b0b193b in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/predModule.cpp:221:30 #12 0x7b3a7b03fcd2 in internal_glmerWrkIter(lme4::merPredD*, lme4::glmResp*, bool) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:274:13 #13 0x7b3a7b03fcd2 in pwrssUpdate(lme4::glmResp*, lme4::merPredD*, bool, double, int, int) /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:330:20 #14 0x7b3a7b03ebc8 in glmerLaplace /data/gannet/ripley/R/packages/tests-clang-ASAN/lme4/src/external.cpp:386:9 #15 0x56086df5fb06 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770:11 #16 0x56086e023d2d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #17 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x56086e00ad28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x56086e063bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #24 0x56086e00a840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x56086e061269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #26 0x56086e00a840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #27 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x56086e02beba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x56086e02beba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #31 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x56086e00c60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x56086e00a4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x56086e00c9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #36 0x56086e00a9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #37 0x56086e063bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #38 0x56086e00a840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #39 0x56086e00c9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #40 0x56086e00a9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #41 0x56086e00c9a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683:12 #42 0x56086e00a9d1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249:20 #43 0x56086e00c60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #44 0x56086e00a2b7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191:2 #45 0x56086e01877a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #46 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #47 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #49 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #50 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #51 0x56086e00ad28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #52 0x56086e061269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #53 0x56086e00a840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #54 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #55 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #56 0x56086e02beba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #57 0x56086e02beba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #58 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #59 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #60 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #61 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #62 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #63 0x56086e00ad28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #64 0x56086dec0abc in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788:12 #65 0x56086e01877a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #66 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #67 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #68 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #69 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #70 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #71 0x56086e00ad28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #72 0x56086e063bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #73 0x56086e00a840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #74 0x56086e068653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #75 0x56086e01877a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #76 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #77 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #78 0x56086e00c60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #79 0x56086e00a4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #80 0x56086e069883 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018:9 #81 0x56086e1124b9 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11 #82 0x56086e01df93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #83 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #84 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #85 0x56086e00c60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #86 0x56086e00a4f5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #87 0x56086e00c60a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #88 0x56086e0371b1 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5867:6 #89 0x56086e0371b1 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7880:20 #90 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #91 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #92 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #93 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #94 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #95 0x56086e00ad28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #96 0x56086e068653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #97 0x56086e01877a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #98 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #99 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #100 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #101 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #102 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #103 0x56086e00ad28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #104 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #105 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #106 0x56086e02beba in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #107 0x56086e02beba in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #108 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #109 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #110 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #111 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #112 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #113 0x56086e00ad28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #114 0x56086e0dbbe1 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #115 0x56086e0de410 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #116 0x56086e0de410 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #117 0x56086e0de4a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #118 0x56086dddfd3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #119 0x7f3a94111574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #120 0x7f3a94111627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #121 0x56086dcf77d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7d6a90a1d530 is located 48 bytes inside of 6448-byte region [0x7d6a90a1d500,0x7d6a90a1ee30) freed by thread T0 here: #0 0x56086dd9c916 in free /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:51:3 #1 0x56086e0f931b in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167:7 #2 0x56086e0f931b in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951:5 #3 0x56086e0ec18b in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237:19 #4 0x56086e101fc5 in CONS_NR /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2519:2 #5 0x56086e0e322a in Rf_matchArgs_NR /data/gannet/ripley/R/svn/R-devel/src/main/match.c:196:12 #6 0x56086e0e4c58 in Rf_matchArgs_RC /data/gannet/ripley/R/svn/R-devel/src/main/match.c:392:17 #7 0x56086e051fa6 in make_applyClosure_env /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2261:15 #8 0x56086e051b25 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2304:19 #9 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #10 0x56086e00ad28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #11 0x56086e05c9cb in do_if /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2709:20 #12 0x56086e00a840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #13 0x56086e061269 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #14 0x56086e00a840 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #15 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #16 0x56086e05c60a in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567:11 #17 0x7f3a911eff40 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154:19 #18 0x56086e121853 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348:13 #19 0x56086e026a1f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085:12 #20 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #21 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #22 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #23 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #24 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #25 0x56086e122e97 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687:10 #26 0x56086e04aa0f in tryDispatch /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6090:16 #27 0x56086e0181c2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8320:19 #28 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #29 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #30 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 previously allocated by thread T0 here: #0 0x56086dd9cbb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x56086e0e6c7c in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894:7 #2 0x56086de3f32b in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #3 0x56086de3f32b in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236:17 #4 0x7b3a878060ce in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676:17 #5 0x56086df54365 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:11 #6 0x56086e01877a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #7 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #8 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #9 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #10 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #11 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #12 0x56086e118e14 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #13 0x56086e117a98 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523:9 #14 0x56086e11a073 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #15 0x56086e01df93 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #16 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #17 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #19 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #20 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #21 0x56086e00ad28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #22 0x56086e068653 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #23 0x56086e01877a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #24 0x56086e00bd74 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #25 0x56086e00a301 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #26 0x56086e052a9c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #27 0x56086e051c58 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #28 0x56086e00d3be in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #29 0x56086e00ad28 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #30 0x56086e063bc5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925:46 in Eigen::internal::product_evaluator, 0, Eigen::Stride<0, 0>> const>, Eigen::Map, 0, Eigen::Stride<0, 0>>, 1>, 8, Eigen::DiagonalShape, Eigen::DenseShape, double, double>::coeff(long, long) const Shadow bytes around the buggy address: 0x7d6a90a1d280: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d6a90a1d300: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d6a90a1d380: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d6a90a1d400: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d6a90a1d480: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d6a90a1d500: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7d6a90a1d580: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d6a90a1d600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d6a90a1d680: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d6a90a1d700: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d6a90a1d780: fd fd fd fd fd fd fd fd fd fd fd fd fd fd 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 ==653434==ABORTING --- re-building ‘lmerperf.Rmd’ using rmarkdown --- finished re-building ‘lmerperf.Rmd’ --- re-building ‘Theory.Rnw’ using knitr --- finished re-building ‘Theory.Rnw’ --- re-building ‘lmer.Rnw’ using knitr --- finished re-building ‘lmer.Rnw’ --- re-building ‘PLSvGLS.Rnw’ using Sweave --- finished re-building ‘PLSvGLS.Rnw’ SUMMARY: processing the following file failed: ‘covariance_structures.Rmd’ Error: Vignette re-building failed. Execution halted * DONE Status: 3 ERRORs