* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/lme4.Rcheck’ * using R Under development (unstable) (2026-07-04 r90207) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-07-05 12:08:38 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 ... [8m/13m] OK * used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ * checking package directory ... OK * checking whether the package can be loaded ... [19s/42s] OK * checking whether the package can be loaded with stated dependencies ... [17s/34s] OK * checking whether the package can be unloaded cleanly ... [17s/28s] OK * checking whether the namespace can be loaded with stated dependencies ... [14s/28s] OK * checking whether the namespace can be unloaded cleanly ... [18s/31s] OK * checking loading without being on the library search path ... [16s/30s] OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [36s/65s] 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)) ================================================================= ==3795135==ERROR: AddressSanitizer: heap-use-after-free on address 0x7d8cd6a408b0 at pc 0x7bccc01d0d9d bp 0x7fff0cf90ee0 sp 0x7fff0cf90ed8 READ of size 8 at 0x7d8cd6a408b0 thread T0 #0 0x7bccc01d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7bccc01d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7bccc01d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7bccc01d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7bccc01d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7bccc01d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7bccc01d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7bccc01d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7bccc01d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7bccc01d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7bccc01d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7bccc0046416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7bccc0046416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7bccc005e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #74 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #75 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #76 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #77 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #78 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #79 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #80 0x7fccda012574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #81 0x7fccda012627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #82 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7d8cd6a408b0 is located 48 bytes inside of 1840-byte region [0x7d8cd6a40880,0x7d8cd6a40fb0) freed by thread T0 here: #0 0x7fccdb6e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a782fb in Rf_cons /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2488 #5 0x0000008975b0 in promiseArgsEx /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3789 #6 0x000000899178 in Rf_promiseArgs /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3854 #7 0x000000899178 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4226 #8 0x000000828e6c in do_as_environment /data/gannet/ripley/R/svn/R-devel/src/main/envir.c:3654 #9 0x0000008639ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1262 #10 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #11 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #12 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #13 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #14 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #15 0x000000882ecd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567 #16 0x7fccd6fcde3a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #17 0x000000ab5d56 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #18 0x0000008f0311 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #19 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #20 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #21 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #22 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #23 0x000000ab91dc in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #24 0x000000ab91dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #25 0x000000899880 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4191 #26 0x000000d0bd6b in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1564 #27 0x000000d6ba7f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264 #28 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #29 0x000000862f2e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1219 #30 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #31 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 previously allocated by thread T0 here: #0 0x7fccdb6e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7bcccc94b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7d8cd6a40600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d8cd6a40680: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d8cd6a40700: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d8cd6a40780: fd fd fd fd fd fd fa fa fa fa fa fa fa fa fa fa 0x7d8cd6a40800: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d8cd6a40880: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7d8cd6a40900: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d8cd6a40980: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d8cd6a40a00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d8cd6a40a80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d8cd6a40b00: 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 ==3795135==ABORTING * checking tests ... [25m/40m] ERROR Running ‘AAAtest-all.R’ [37s/79s] Running ‘HSAURtrees.R’ [20s/35s] Running ‘REMLdev.R’ [17s/34s] Running ‘ST.R’ [18s/29s] Running ‘agridat_gotway.R’ [19s/27s] Running ‘bootMer.R’ [54s/123s] Running ‘boundary.R’ [136s/234s] Running ‘confint.R’ [37s/57s] Running ‘devCritFun.R’ [17s/30s] Running ‘drop.R’ [23s/35s] Running ‘drop1contrasts.R’ [21s/39s] Running ‘dynload.R’ [49s/75s] Running ‘elston.R’ [24s/33s] Running ‘evalCall.R’ [20s/32s] Running ‘extras.R’ [17s/26s] Running ‘falsezero_dorie.R’ [19s/28s] Running ‘fewlevels.R’ Running ‘getME.R’ [23s/33s] Running ‘glmer-1.R’ [20s/29s] Running ‘glmerControlPass.R’ [36s/53s] Running ‘glmerWarn.R’ [30s/49s] Running ‘glmmExt.R’ [59s/97s] Running ‘glmmWeights.R’ [29s/45s] Running ‘hatvalues.R’ [19s/28s] Running ‘is.R’ [22s/32s] Running ‘lmList-tst.R’ [20s/31s] Running ‘lme4_nlme.R’ [20s/33s] Running ‘lmer-0.R’ [21s/32s] Running ‘lmer-1.R’ [19s/31s] Running ‘lmer-conv.R’ [18s/26s] Running ‘lmer2_ex.R’ [17s/25s] Running ‘methods.R’ [27s/40s] Running ‘minval.R’ [18s/29s] Running ‘modFormula.R’ [30s/46s] Running ‘nbinom.R’ [17s/30s] Running ‘nlmer-conv.R’ [18s/25s] Running ‘nlmer.R’ [20s/28s] Running ‘offset.R’ [27s/39s] Running ‘optimizer.R’ [28s/46s] Running ‘polytomous.R’ [18s/27s] Running ‘prLogistic.R’ [19s/31s] Running ‘predict_basis.R’ [24s/38s] Running ‘predsim.R’ [25s/41s] Running ‘priorWeights.R’ [49s/77s] Running ‘priorWeightsModComp.R’ [32s/46s] Running ‘profile-tst.R’ [18s/28s] Running ‘refit.R’ [17s/27s] Running ‘resids.R’ [20s/32s] Running ‘respiratory.R’ [26s/45s] Running ‘simulate.R’ [19s/28s] Running ‘test-glmernbref.R’ [34s/54s] Running ‘testOptControl.R’ [19s/31s] Running ‘testcolonizer.R’ [22s/32s] Running ‘testcrab.R’ [25s/33s] Running ‘throw.R’ [32s/46s] Running ‘varcorr.R’ [22s/33s] Running ‘vcov-etc.R’ [20s/30s] 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" ) + } ================================================================= ==3801279==ERROR: AddressSanitizer: heap-use-after-free on address 0x7d05aa6c50b0 at pc 0x7b4593bd0d9d bp 0x7ffcca2771c0 sp 0x7ffcca2771b8 READ of size 8 at 0x7d05aa6c50b0 thread T0 #0 0x7b4593bd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7b4593bd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7b4593bd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7b4593bd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7b4593bd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7b4593bd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7b4593bd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7b4593bd0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7b4593bd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7b4593bd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7b4593bd0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7b4593a46416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7b4593a46416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7b4593a5e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #33 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #34 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #35 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #39 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #40 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #41 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #42 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #43 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #44 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #45 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #46 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #47 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #48 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #49 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #50 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #51 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #53 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #54 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #55 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #56 0x00000089d693 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993 #57 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #58 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #59 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #60 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #61 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #62 0x00000088091a in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #63 0x00000088091a in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2465 #64 0x000000499fd6 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75 #65 0x000000a9e436 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424 #66 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #67 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #68 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #69 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #70 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #71 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #72 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #73 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #74 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #75 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #76 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #77 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #78 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #79 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #80 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #81 0x7f45adc12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #82 0x7f45adc12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7d05aa6c50b0 is located 48 bytes inside of 1840-byte region [0x7d05aa6c5080,0x7d05aa6c57b0) freed by thread T0 here: #0 0x7f45af2e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a88f6e in Rf_mkPROMISE /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2613 #5 0x0000008ec38c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8003 #6 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #7 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #8 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #9 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #10 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #11 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #12 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #13 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #14 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #15 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #16 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #17 0x000000882ecd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567 #18 0x7f45aa928e3a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #19 0x000000ab5d56 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #20 0x0000008f0311 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #21 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #22 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #24 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #25 0x000000ab91dc in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #26 0x000000ab91dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #27 0x00000089b0be in tryDispatch /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6090 #28 0x0000008ce28f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8320 #29 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #30 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #31 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 previously allocated by thread T0 here: #0 0x7f45af2e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7b459c54b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7d05aa6c4e00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d05aa6c4e80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d05aa6c4f00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d05aa6c4f80: fd fd fd fd fd fd fa fa fa fa fa fa fa fa fa fa 0x7d05aa6c5000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d05aa6c5080: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7d05aa6c5100: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d05aa6c5180: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d05aa6c5200: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d05aa6c5280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d05aa6c5300: 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 ==3801279==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 ================================================================= ==3819436==ERROR: AddressSanitizer: heap-use-after-free on address 0x7df7a44c0930 at pc 0x7ba7801d0d9d bp 0x7ffce8b7e8f0 sp 0x7ffce8b7e8e8 READ of size 8 at 0x7df7a44c0930 thread T0 #0 0x7ba7801d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7ba7801d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7ba7801d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7ba7801d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7ba7801d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7ba7801d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7ba7801d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7ba7801d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7ba7801d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7ba7801d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7ba7801d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7ba780046416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7ba780046416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7ba78005e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #74 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #75 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #76 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #77 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #78 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #79 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #80 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #81 0x7fa79a012574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #82 0x7fa79a012627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7df7a44c0930 is located 48 bytes inside of 8240-byte region [0x7df7a44c0900,0x7df7a44c2930) freed by thread T0 here: #0 0x7fa79b8e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a782fb in Rf_cons /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2488 #5 0x00000080993d in Rf_defineVar /data/gannet/ripley/R/svn/R-devel/src/main/envir.c:1996 #6 0x000000882d02 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2544 #7 0x7fa79712be3a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #8 0x000000ab5d56 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #9 0x0000008f0311 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #10 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #11 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #12 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #13 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #14 0x000000ab91dc in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #15 0x000000ab91dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #16 0x000000899880 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4191 #17 0x000000d0bd6b in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1564 #18 0x000000d6ba7f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264 #19 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #20 0x000000862f2e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1219 #21 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #22 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #23 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #24 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #25 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #26 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #27 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #28 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #30 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 previously allocated by thread T0 here: #0 0x7fa79b8e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7ba78894b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7df7a44c0680: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7df7a44c0700: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7df7a44c0780: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7df7a44c0800: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7df7a44c0880: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7df7a44c0900: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7df7a44c0980: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7df7a44c0a00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7df7a44c0a80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7df7a44c0b00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7df7a44c0b80: 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 ==3819436==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) ================================================================= ==3869517==ERROR: AddressSanitizer: heap-use-after-free on address 0x7cfffbbaf8b0 at pc 0x7b3fe51d0d9d bp 0x7fff9c42c790 sp 0x7fff9c42c788 READ of size 8 at 0x7cfffbbaf8b0 thread T0 #0 0x7b3fe51d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7b3fe51d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7b3fe51d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7b3fe51d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7b3fe51d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7b3fe51d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7b3fe51d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7b3fe51d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7b3fe51d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7b3fe51d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7b3fe51d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7b3fe5046416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7b3fe5046416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7b3fe5060c03 in glmerAGQ /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:428 #14 0x00000074ffa0 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:775 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x00000089d693 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993 #74 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #75 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #76 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #77 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #78 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #79 0x00000089f4c3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018 #80 0x000000a9e436 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424 #81 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #82 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #83 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #84 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #85 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #86 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #87 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #88 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #89 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #90 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #91 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #92 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #93 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #94 0x7f3fff012574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #95 0x7f3fff012627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #96 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7cfffbbaf8b0 is located 48 bytes inside of 1840-byte region [0x7cfffbbaf880,0x7cfffbbaffb0) freed by thread T0 here: #0 0x7f40006e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a872bb in CONS_NR /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2519 #5 0x0000008e18ea in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8059 #6 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #7 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #8 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #9 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #10 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #11 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #12 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #13 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #14 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #15 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #16 0x000000882ecd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567 #17 0x7f3ffbd4ee3a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #18 0x000000ab5d56 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #19 0x0000008f0311 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #20 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #21 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #22 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #23 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #24 0x000000ab91dc in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #25 0x000000ab91dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #26 0x000000899880 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4191 #27 0x000000d0bd6b in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1564 #28 0x000000d6ba7f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264 #29 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #30 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #31 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 previously allocated by thread T0 here: #0 0x7f40006e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7b3fed94b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000089d693 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7cfffbbaf600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cfffbbaf680: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cfffbbaf700: fd fd fd fd fd fd fd fd fd fd fd fa fa fa fa fa 0x7cfffbbaf780: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7cfffbbaf800: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7cfffbbaf880: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7cfffbbaf900: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cfffbbaf980: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cfffbbafa00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cfffbbafa80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cfffbbafb00: 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 ==3869517==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) ================================================================= ==3902716==ERROR: AddressSanitizer: heap-use-after-free on address 0x7d9adc3a40b0 at pc 0x7bdac59d0d9d bp 0x7ffcda059a50 sp 0x7ffcda059a48 READ of size 8 at 0x7d9adc3a40b0 thread T0 #0 0x7bdac59d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7bdac59d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7bdac59d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7bdac59d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7bdac59d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7bdac59d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7bdac59d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7bdac59d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7bdac59d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7bdac59d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7bdac59d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7bdac5846416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7bdac5846416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7bdac585e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x00000089d693 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993 #74 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #75 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #76 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #77 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #78 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #79 0x00000089f4c3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018 #80 0x000000a9e436 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424 #81 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #82 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #83 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #84 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #85 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #86 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #87 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #88 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #89 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #90 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #91 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #92 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #93 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #94 0x7fdadf812574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #95 0x7fdadf812627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #96 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7d9adc3a40b0 is located 48 bytes inside of 1840-byte region [0x7d9adc3a4080,0x7d9adc3a47b0) freed by thread T0 here: #0 0x7fdae0ee5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a9428b in Rf_allocSExp /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2448 #5 0x0000007a6ee9 in Rf_allocSExp /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2443 #6 0x0000007a6ee9 in duplicate1 /data/gannet/ripley/R/svn/R-devel/src/main/duplicate.c:304 #7 0x00000085aea7 in Rf_duplicate /data/gannet/ripley/R/svn/R-devel/src/main/duplicate.c:141 #8 0x00000085aea7 in R_withCallingErrorHandler /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:2592 #9 0x7fdadc54e73f in R_evalHandleError /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:93 #10 0x7fdadc54e73f in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1109 #11 0x000000ab5d56 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #12 0x0000008f0311 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #13 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #14 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #15 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #16 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #17 0x000000ab91dc in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #18 0x000000ab91dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #19 0x000000899880 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4191 #20 0x000000d0bd6b in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1564 #21 0x000000d6ba7f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264 #22 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #23 0x000000862f2e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1219 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 previously allocated by thread T0 here: #0 0x7fdae0ee6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7bdace14b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000089d693 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7d9adc3a3e00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d9adc3a3e80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d9adc3a3f00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d9adc3a3f80: 00 00 00 00 00 00 00 00 00 00 00 fa fa fa fa fa 0x7d9adc3a4000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d9adc3a4080: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7d9adc3a4100: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d9adc3a4180: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d9adc3a4200: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d9adc3a4280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d9adc3a4300: 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 ==3902716==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 ================================================================= ==3906775==ERROR: AddressSanitizer: heap-use-after-free on address 0x7e9df7100830 at pc 0x7b5de09d0d9d bp 0x7ffd4b429c80 sp 0x7ffd4b429c78 READ of size 8 at 0x7e9df7100830 thread T0 #0 0x7b5de09d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7b5de09d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7b5de09d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7b5de09d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7b5de09d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7b5de09d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7b5de09d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7b5de09d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7b5de09d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7b5de09d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7b5de09d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7b5de0846416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7b5de0846416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7b5de085e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #74 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #75 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #76 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #77 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #78 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #79 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #80 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #81 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #82 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #83 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #84 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #85 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #86 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #87 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #88 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #89 0x7f5dfa612574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #90 0x7f5dfa612627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #91 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7e9df7100830 is located 48 bytes inside of 129024-byte region [0x7e9df7100800,0x7e9df7120000) freed by thread T0 here: #0 0x7f5dfbee5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a872bb in CONS_NR /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2519 #5 0x000000895369 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3685 #6 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #7 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #8 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #13 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #14 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #15 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #16 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #17 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #18 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #19 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #20 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #21 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #22 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #23 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #24 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #25 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #26 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #27 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #28 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #29 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #30 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 previously allocated by thread T0 here: #0 0x7f5dfbee6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7b5de8f4b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7e9df7100580: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e9df7100600: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e9df7100680: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e9df7100700: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e9df7100780: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7e9df7100800: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7e9df7100880: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e9df7100900: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e9df7100980: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e9df7100a00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e9df7100a80: 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 ==3906775==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")) ================================================================= ==3913923==ERROR: AddressSanitizer: heap-use-after-free on address 0x7e711b844430 at pc 0x7b91047d0d9d bp 0x7ffe65661e70 sp 0x7ffe65661e68 READ of size 8 at 0x7e711b844430 thread T0 #0 0x7b91047d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7b91047d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7b91047d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7b91047d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7b91047d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7b91047d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7b91047d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7b91047d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7b91047d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7b91047d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7b91047d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7b9104646416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7b9104646416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7b910465e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x00000089d693 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993 #74 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #75 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #76 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #77 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #78 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #79 0x00000089f4c3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018 #80 0x000000a9e436 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424 #81 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #82 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #83 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #84 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #85 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #86 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #87 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #88 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #89 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #90 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #91 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #92 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #93 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #94 0x7f911e612574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #95 0x7f911e612627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #96 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7e711b844430 is located 48 bytes inside of 41648-byte region [0x7e711b844400,0x7e711b84e6b0) freed by thread T0 here: #0 0x7f911fee5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a782fb in Rf_cons /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2488 #5 0x00000085b08b in R_withCallingErrorHandler /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:2603 #6 0x7f911b52873f in R_evalHandleError /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:93 #7 0x7f911b52873f in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1109 #8 0x000000ab5d56 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #9 0x0000008f0311 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #10 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #11 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #12 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #13 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #14 0x000000ab91dc in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #15 0x000000ab91dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #16 0x000000899880 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4191 #17 0x000000d0bd6b in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1564 #18 0x000000d6ba7f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264 #19 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #20 0x000000862f2e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1219 #21 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #22 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #23 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #24 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #25 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #26 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #27 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #28 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #30 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #31 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 previously allocated by thread T0 here: #0 0x7f911fee6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7b910cf4b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000089d693 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7e711b844180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e711b844200: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e711b844280: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e711b844300: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e711b844380: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7e711b844400: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7e711b844480: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e711b844500: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e711b844580: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e711b844600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e711b844680: 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 ==3913923==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 ================================================================= ==3925487==ERROR: AddressSanitizer: heap-use-after-free on address 0x7e6b211a0430 at pc 0x7b8b09fd0d9d bp 0x7fff8d1d94b0 sp 0x7fff8d1d94a8 READ of size 8 at 0x7e6b211a0430 thread T0 #0 0x7b8b09fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7b8b09fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7b8b09fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7b8b09fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7b8b09fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7b8b09fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7b8b09fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7b8b09fd0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7b8b09fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7b8b09fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7b8b09fd0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7b8b09e46416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7b8b09e46416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7b8b09e5e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #74 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #75 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #76 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #77 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #78 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #79 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #80 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #81 0x7f8b23e12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #82 0x7f8b23e12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7e6b211a0430 is located 48 bytes inside of 41648-byte region [0x7e6b211a0400,0x7e6b211aa6b0) freed by thread T0 here: #0 0x7f8b256e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a872bb in CONS_NR /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2519 #5 0x000000895369 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3685 #6 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #7 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #8 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #9 0x000000874a92 in do_if /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2709 #10 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #11 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #12 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #13 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #14 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #15 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #16 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #17 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #18 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #19 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #20 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #21 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #22 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #23 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #24 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #25 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #26 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #27 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #28 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #29 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 previously allocated by thread T0 here: #0 0x7f8b256e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7b8b1274b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7e6b211a0180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e6b211a0200: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e6b211a0280: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e6b211a0300: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e6b211a0380: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7e6b211a0400: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7e6b211a0480: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e6b211a0500: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e6b211a0580: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e6b211a0600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e6b211a0680: 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 ==3925487==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 ================================================================= ==3983781==ERROR: AddressSanitizer: heap-use-after-free on address 0x7d3c2f3cd0b0 at pc 0x7b7c189d0d9d bp 0x7fff46e042d0 sp 0x7fff46e042c8 READ of size 8 at 0x7d3c2f3cd0b0 thread T0 #0 0x7b7c189d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7b7c189d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7b7c189d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7b7c189d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7b7c189d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7b7c189d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7b7c189d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7b7c189d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7b7c189d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7b7c189d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7b7c189d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7b7c18846416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7b7c18846416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7b7c1885e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #33 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #34 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #35 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #36 0x7b7c210da938 in port_nlminb /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/port.c:420 #37 0x00000074fcb6 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:790 #38 0x000000754a0a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #39 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #40 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #41 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #42 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #43 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #44 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #45 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #46 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #47 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #48 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #49 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #50 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #51 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #52 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #53 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #54 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #55 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #56 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #57 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #58 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #59 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #60 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #61 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #62 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #63 0x000000aa52d3 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:509 #64 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #65 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #66 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #67 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #68 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #69 0x000000882ecd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567 #70 0x7f7c2f74ee3a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #71 0x000000ab5d56 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #72 0x0000008639ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1262 #73 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #74 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #75 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #76 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #77 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #78 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #79 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #80 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #81 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #82 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #83 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #84 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #85 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #86 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #87 0x7f7c32812574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #88 0x7f7c32812627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #89 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7d3c2f3cd0b0 is located 48 bytes inside of 1840-byte region [0x7d3c2f3cd080,0x7d3c2f3cd7b0) freed by thread T0 here: #0 0x7f7c340e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a7d73a in R_gc /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3091 #5 0x000000a7d73a in do_gc /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2131 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #13 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #14 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #15 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #16 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #17 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #18 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #19 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #20 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #21 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #22 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #23 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #24 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #25 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #26 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #27 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #28 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #29 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #30 0x000000aa52d3 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:509 #31 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #32 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #33 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 previously allocated by thread T0 here: #0 0x7f7c340e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7b7c2114b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #32 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #33 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7d3c2f3cce00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d3c2f3cce80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d3c2f3ccf00: fd fd fd fd fd fd fd fd fd fd fd fa fa fa fa fa 0x7d3c2f3ccf80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d3c2f3cd000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d3c2f3cd080: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7d3c2f3cd100: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d3c2f3cd180: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d3c2f3cd200: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d3c2f3cd280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d3c2f3cd300: 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 ==3983781==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) ================================================================= ==4031881==ERROR: AddressSanitizer: heap-use-after-free on address 0x7e697fe12230 at pc 0x7bc9691d0d9d bp 0x7ffcc1cfae50 sp 0x7ffcc1cfae48 READ of size 8 at 0x7e697fe12230 thread T0 #0 0x7bc9691d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7bc9691d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7bc9691d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7bc9691d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7bc9691d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7bc9691d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7bc9691d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7bc9691d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7bc9691d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7bc9691d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7bc9691d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7bc969046416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7bc969046416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7bc96905e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #74 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #75 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #76 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #77 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #78 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #79 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #80 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #81 0x7fc983012574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #82 0x7fc983012627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7e697fe12230 is located 48 bytes inside of 21360-byte region [0x7e697fe12200,0x7e697fe17570) freed by thread T0 here: #0 0x7fc9848e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a88f6e in Rf_mkPROMISE /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2613 #5 0x000000882a93 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2538 #6 0x7fc97ff28e3a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #7 0x000000ab5d56 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #8 0x0000008f0311 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #9 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #10 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #11 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #12 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #13 0x000000ab91dc in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #14 0x000000ab91dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #15 0x000000899880 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4191 #16 0x000000d0bd6b in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1564 #17 0x000000d6ba7f in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1264 #18 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #19 0x000000862f2e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1219 #20 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #21 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #22 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #23 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #24 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #25 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #26 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #27 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #28 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #29 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #30 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 previously allocated by thread T0 here: #0 0x7fc9848e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7bc97194b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7e697fe11f80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e697fe12000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e697fe12080: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e697fe12100: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e697fe12180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7e697fe12200: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7e697fe12280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e697fe12300: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e697fe12380: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e697fe12400: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e697fe12480: 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 ==4031881==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) ================================================================= ==4048105==ERROR: AddressSanitizer: heap-use-after-free on address 0x7e16d0c3e130 at pc 0x7bd6ba1d0d9d bp 0x7ffe9fab01e0 sp 0x7ffe9fab01d8 READ of size 8 at 0x7e16d0c3e130 thread T0 #0 0x7bd6ba1d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7bd6ba1d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7bd6ba1d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7bd6ba1d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7bd6ba1d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7bd6ba1d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7bd6ba1d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7bd6ba1d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7bd6ba1d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7bd6ba1d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7bd6ba1d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7bd6ba046416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7bd6ba046416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7bd6ba05e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #74 0x0000008a9bb1 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #75 0x0000008a9bb1 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5867 #76 0x0000008e6b7c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7880 #77 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #78 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #79 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #80 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #81 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #82 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #83 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #84 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #85 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #86 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #87 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #88 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #89 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #90 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #91 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #92 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #93 0x7fd6d4012574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #94 0x7fd6d4012627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #95 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7e16d0c3e130 is located 48 bytes inside of 7664-byte region [0x7e16d0c3e100,0x7e16d0c3fef0) freed by thread T0 here: #0 0x7fd6d56e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a872bb in CONS_NR /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2519 #5 0x0000008e18ea in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8059 #6 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #7 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #8 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #9 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #10 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #11 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #12 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #13 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #14 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #15 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #16 0x000000882ecd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2567 #17 0x7fd6d0d28e3a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #18 0x000000ab5d56 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #19 0x0000008f0311 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #20 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #21 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #22 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #23 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #24 0x000000ab91dc in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #25 0x000000ab91dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #26 0x00000089b0be in tryDispatch /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6090 #27 0x0000008ce28f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8320 #28 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #29 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #31 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 previously allocated by thread T0 here: #0 0x7fd6d56e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7bd6c294b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7e16d0c3de80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e16d0c3df00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e16d0c3df80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e16d0c3e000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e16d0c3e080: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7e16d0c3e100: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7e16d0c3e180: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e16d0c3e200: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e16d0c3e280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e16d0c3e300: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e16d0c3e380: 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 ==4048105==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 ? + + } ================================================================= ==4050498==ERROR: AddressSanitizer: heap-use-after-free on address 0x7e8d1c594430 at pc 0x7bad059d0d9d bp 0x7ffe847adb60 sp 0x7ffe847adb58 READ of size 8 at 0x7e8d1c594430 thread T0 #0 0x7bad059d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7bad059d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7bad059d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7bad059d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7bad059d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7bad059d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7bad059d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7bad059d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7bad059d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7bad059d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7bad059d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7bad05846416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7bad05846416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7bad0585e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #74 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #75 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #76 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #77 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #78 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #79 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #80 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #81 0x7fad1f812574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #82 0x7fad1f812627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #83 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7e8d1c594430 is located 48 bytes inside of 41648-byte region [0x7e8d1c594400,0x7e8d1c59e6b0) freed by thread T0 here: #0 0x7fad210e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a7909d in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2710 #5 0x00000081d009 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #6 0x00000081d009 in do_missing /data/gannet/ripley/R/svn/R-devel/src/main/envir.c:2789 #7 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #8 0x000000874a92 in do_if /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2709 #9 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #10 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #11 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #12 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #13 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #14 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #15 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #16 0x0000007f6c93 in getActiveValue /data/gannet/ripley/R/svn/R-devel/src/main/envir.c:168 #17 0x0000007f6c93 in BINDING_VALUE /data/gannet/ripley/R/svn/R-devel/src/main/envir.c:119 #18 0x0000007f6c93 in R_HashGet /data/gannet/ripley/R/svn/R-devel/src/main/envir.c:298 #19 0x0000007ffb6f in R_findVarInFrame /data/gannet/ripley/R/svn/R-devel/src/main/envir.c:1249 #20 0x0000007ffb6f in R_findVar /data/gannet/ripley/R/svn/R-devel/src/main/envir.c:1387 #21 0x000000862efa in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1175 #22 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #23 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #24 0x000000874a92 in do_if /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2709 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #27 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #28 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #29 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #30 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #31 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #32 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #33 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #34 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 previously allocated by thread T0 here: #0 0x7fad210e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7bad0e14b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7e8d1c594180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e8d1c594200: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e8d1c594280: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e8d1c594300: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e8d1c594380: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7e8d1c594400: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7e8d1c594480: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e8d1c594500: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e8d1c594580: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e8d1c594600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7e8d1c594680: 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 ==4050498==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) ================================================================= ==4053437==ERROR: AddressSanitizer: heap-use-after-free on address 0x7cd4c6fa80b0 at pc 0x7b14b03d0d9d bp 0x7ffd0b498710 sp 0x7ffd0b498708 READ of size 8 at 0x7cd4c6fa80b0 thread T0 #0 0x7b14b03d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7b14b03d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7b14b03d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7b14b03d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7b14b03d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7b14b03d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7b14b03d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7b14b03d0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7b14b03d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7b14b03d0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7b14b03d0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7b14b0246416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7b14b0246416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7b14b025e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #33 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #34 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #35 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #39 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #40 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #41 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #42 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #43 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #44 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #45 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #46 0x7f14ca212574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #47 0x7f14ca212627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #48 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7cd4c6fa80b0 is located 48 bytes inside of 1840-byte region [0x7cd4c6fa8080,0x7cd4c6fa87b0) freed by thread T0 here: #0 0x7f14cb8e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a782fb in Rf_cons /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2488 #5 0x7b14b316cccc in Rcpp::Rcpp_precious_preserve(SEXPREC*) /tmp/RtmpRy9VNC/R.INSTALL28e46352768c10/Rcpp/src/barrier.cpp:115 #6 0x7b14b025dc8c in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:380 #7 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #8 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #9 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #10 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #11 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #12 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #13 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #14 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #15 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #16 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #17 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #18 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #23 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #24 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #25 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #26 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #27 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #28 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #29 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #30 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #31 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 previously allocated by thread T0 here: #0 0x7f14cb8e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7b14b8b4b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7cd4c6fa7e00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd4c6fa7e80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd4c6fa7f00: fd fd fd fd fd fd fd fd fd fd fd fa fa fa fa fa 0x7cd4c6fa7f80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7cd4c6fa8000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7cd4c6fa8080: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7cd4c6fa8100: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd4c6fa8180: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd4c6fa8200: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd4c6fa8280: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7cd4c6fa8300: 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 ==4053437==ABORTING * checking package vignettes ... OK * checking re-building of vignette outputs ... [23m/30m] 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 ================================================================= ==4069286==ERROR: AddressSanitizer: heap-use-after-free on address 0x7dd63e47f530 at pc 0x7ba625fd0d9d bp 0x7ffe62754f20 sp 0x7ffe62754f18 READ of size 8 at 0x7dd63e47f530 thread T0 #0 0x7ba625fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 #1 0x7ba625fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654 #2 0x7ba625fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668 #3 0x7ba625fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347 #4 0x7ba625fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785 #5 0x7ba625fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954 #6 0x7ba625fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890 #7 0x7ba625fd0d9c 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>, Eigen::internal::evaluator_traits, 0, Eigen::Stride<0, 0> > const>, Eigen::Map, 0, Eigen::Stride<0, 0> >, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858 #8 0x7ba625fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836 #9 0x7ba625fd0d9c 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-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66 #10 0x7ba625fd0d9c in lme4::merPredD::updateXwts(Eigen::Array const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:221 #11 0x7ba625e46416 in internal_glmerWrkIter /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:274 #12 0x7ba625e46416 in pwrssUpdate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:330 #13 0x7ba625e5e3d4 in glmerLaplace /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:386 #14 0x00000075005e in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #15 0x0000008ed70a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #19 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #20 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #21 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #25 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #26 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #27 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #28 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #29 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #30 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #31 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #34 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #35 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #36 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #37 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #38 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #39 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #40 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #41 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #42 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #43 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #44 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #45 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #46 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #48 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #49 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #50 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #51 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #52 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #53 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #54 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #55 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #56 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #57 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #58 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #60 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #61 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #62 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x0000006237b5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2788 #64 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #65 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #66 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #68 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #69 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #70 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #71 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #72 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #73 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #74 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #75 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #76 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #77 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #78 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #79 0x00000089f4c3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018 #80 0x000000a9e436 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424 #81 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #82 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #83 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #84 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #85 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #86 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #87 0x0000008a9bb1 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #88 0x0000008a9bb1 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5867 #89 0x0000008e6b7c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7880 #90 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #91 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #92 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #93 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #94 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #95 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #96 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #97 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #98 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #99 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #100 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #101 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #102 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #103 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #104 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #105 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #106 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #107 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #108 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #109 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #110 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #111 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #112 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #113 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #114 0x000000a0b688 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #115 0x000000a0b688 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #116 0x000000a1a97a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #117 0x000000a1aa12 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #118 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #119 0x7fa641a12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #120 0x7fa641a12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #121 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: f060bf4ee83b802127121439cefaeb137652c0ab) 0x7dd63e47f530 is located 48 bytes inside of 6448-byte region [0x7dd63e47f500,0x7dd63e480e30) freed by thread T0 here: #0 0x7fa6432e5beb in free.part.0 (/lib64/libasan.so.8+0xe5beb) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a1bf9f in ReleaseLargeFreeVectors /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1167 #2 0x000000a49e0d in RunGenCollect /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:1951 #3 0x000000a7244d in R_gc_internal /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3237 #4 0x000000a782fb in Rf_cons /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2488 #5 0x0000008977dd in promiseArgsEx /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3840 #6 0x000000863049 in Rf_promiseArgs /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3854 #7 0x000000863049 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1276 #8 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #9 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #10 0x00000087729b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #11 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #12 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #13 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #14 0x00000088038b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #15 0x0000008eb805 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121 #16 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #17 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #19 0x00000086405c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185 #20 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #21 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #22 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #23 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #24 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #25 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #26 0x0000008952f4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3683 #27 0x00000086388c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1249 #28 0x000000930ad1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #29 0x000000863f37 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1191 #30 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 previously allocated by thread T0 here: #0 0x7fa6432e6f2b in malloc (/lib64/libasan.so.8+0xe6f2b) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x000000a7a3e0 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2894 #2 0x0000005077b3 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #3 0x0000005077b3 in Rf_allocMatrix /data/gannet/ripley/R/svn/R-devel/src/main/array.c:236 #4 0x7ba63434b36e in modelmatrix /data/gannet/ripley/R/svn/R-devel/src/library/stats/src/model.c:676 #5 0x00000073b52a in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #6 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #7 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #8 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #9 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #10 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #11 0x000000a9f646 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #12 0x000000a9f646 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #13 0x000000aa3480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #14 0x000000aa56c0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #15 0x000000aa6026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #16 0x0000008e3f11 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #17 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #18 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #20 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #21 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #22 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #24 0x0000008d6d02 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #25 0x0000008c3f63 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #26 0x0000008629ea in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000087ad2a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #28 0x00000087ecdd in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #29 0x000000863098 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #30 0x000000863098 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #31 0x000000894a2e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #32 0x0000008634c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #33 0x00000089c5a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 SUMMARY: AddressSanitizer: heap-use-after-free /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925 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: 0x7dd63e47f280: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dd63e47f300: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dd63e47f380: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dd63e47f400: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dd63e47f480: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7dd63e47f500: fd fd fd fd fd fd[fd]fd fd fd fd fd fd fd fd fd 0x7dd63e47f580: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7dd63e47f600: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7dd63e47f680: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7dd63e47f700: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7dd63e47f780: 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 ==4069286==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