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Type 'q()' to quit R. > 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