==3533511== Memcheck, a memory error detector ==3533511== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. ==3533511== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info ==3533511== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R -f glmmWeights.R --restore --save --no-readline --vanilla ==3533511== R Under development (unstable) (2026-07-02 r90204) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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 ==3533511== Invalid read of size 8 ==3533511== at 0x247DA545: coeff (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925) ==3533511== by 0x247DA545: assignCoeff (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654) ==3533511== by 0x247DA545: assignCoeffByOuterInner (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668) ==3533511== by 0x247DA545: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347) ==3533511== by 0x247DA545: call_dense_assignment_loop >, Eigen::Product > >, Eigen::Map >, 1>, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785) ==3533511== by 0x247DA545: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3533511== by 0x247DA545: call_assignment_no_alias >, Eigen::Product > >, Eigen::Map >, 1>, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3533511== by 0x247DA545: call_assignment >, Eigen::Product > >, Eigen::Map >, 1>, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3533511== by 0x247DA545: call_assignment >, Eigen::Product > >, Eigen::Map >, 1> > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3533511== by 0x247DA545: operator= > >, Eigen::Map >, 1> > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Assign.h:66) ==3533511== by 0x247DA545: lme4::merPredD::updateXwts(Eigen::Array const&) (packages/tests-vg/lme4/src/predModule.cpp:221) ==3533511== by 0x247B2A2F: internal_glmerWrkIter (packages/tests-vg/lme4/src/external.cpp:274) ==3533511== by 0x247B2A2F: pwrssUpdate (packages/tests-vg/lme4/src/external.cpp:330) ==3533511== by 0x247B8E6C: glmerLaplace (packages/tests-vg/lme4/src/external.cpp:386) ==3533511== by 0x4A91E9: R_doDotCall (svn/R-devel/src/main/dotcode.c:770) ==3533511== by 0x4E4283: bcEval_loop (svn/R-devel/src/main/eval.c:8700) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3533511== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3533511== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3533511== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3533511== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3533511== by 0x4F96BC: do_set (svn/R-devel/src/main/eval.c:3585) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== Address 0x25c9b070 is 48 bytes inside a block of size 41,648 free'd ==3533511== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3533511== by 0x5354C5: ReleaseLargeFreeVectors (svn/R-devel/src/main/memory.c:1167) ==3533511== by 0x5354C5: RunGenCollect (svn/R-devel/src/main/memory.c:1951) ==3533511== by 0x5354C5: R_gc_internal (svn/R-devel/src/main/memory.c:3237) ==3533511== by 0x53830B: CONS_NR (svn/R-devel/src/main/memory.c:2519) ==3533511== by 0x52D9A2: Rf_matchArgs_NR (svn/R-devel/src/main/match.c:196) ==3533511== by 0x52E1B8: Rf_matchArgs_RC (svn/R-devel/src/main/match.c:392) ==3533511== by 0x4D7080: make_applyClosure_env (svn/R-devel/src/main/eval.c:2261) ==3533511== by 0x4F7251: applyClosure_core (svn/R-devel/src/main/eval.c:2304) ==3533511== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3533511== by 0x4F7D61: do_if (svn/R-devel/src/main/eval.c:2709) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== by 0x4F80E4: do_begin (svn/R-devel/src/main/eval.c:3001) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== Block was alloc'd at ==3533511== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3533511== by 0x539581: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2894) ==3533511== by 0x44084B: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3533511== by 0x44084B: Rf_allocMatrix (svn/R-devel/src/main/array.c:236) ==3533511== by 0x162E0DA3: modelmatrix (svn/R-devel/src/library/stats/src/model.c:676) ==3533511== by 0x4A76CE: do_External (svn/R-devel/src/main/dotcode.c:573) ==3533511== by 0x4E63CC: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3533511== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3533511== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3533511== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3533511== by 0x4F7D21: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x53FD2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3533511== ==3533511== Invalid read of size 16 ==3533511== at 0x247D31F4: ploadu (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:603) ==3533511== by 0x247D31F4: ploadt (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:969) ==3533511== by 0x247D31F4: load (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/BlasUtil.h:203) ==3533511== by 0x247D31F4: Eigen::internal::general_matrix_vector_product, 0, false, double, Eigen::internal::const_blas_data_mapper, false, 0>::run(long, long, Eigen::internal::const_blas_data_mapper const&, Eigen::internal::const_blas_data_mapper const&, double*, long, double) [clone .isra.0] (R-devel/site-library/RcppEigen/include/Eigen/src/Core/products/GeneralMatrixVector.h:177) ==3533511== by 0x247E7D5B: run >, Eigen::Matrix, Eigen::Matrix > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GeneralProduct.h:253) ==3533511== by 0x247E7D5B: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:388) ==3533511== by 0x247E7D5B: void Eigen::internal::generic_product_impl, 0, Eigen::Stride<0, 0> >, Eigen::Matrix, Eigen::DenseShape, Eigen::DenseShape, 7>::scaleAndAddTo >(Eigen::Matrix&, Eigen::Map, 0, Eigen::Stride<0, 0> > const&, Eigen::Matrix const&, double const&) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:376) ==3533511== by 0x247DD3BE: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:361) ==3533511== by 0x247DD3BE: evalTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:349) ==3533511== by 0x247DD3BE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:148) ==3533511== by 0x247DD3BE: call_assignment_no_alias, Eigen::Product >, Eigen::Matrix, 0>, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3533511== by 0x247DD3BE: run, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:223) ==3533511== by 0x247DD3BE: call_assignment_no_alias, Eigen::CwiseBinaryOp, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3533511== by 0x247DD3BE: _set_noalias, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797) ==3533511== by 0x247DD3BE: PlainObjectBase, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:594) ==3533511== by 0x247DD3BE: Matrix, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:423) ==3533511== by 0x247DD3BE: lme4::merPredD::linPred(double const&) const (packages/tests-vg/lme4/src/predModule.cpp:95) ==3533511== by 0x247B286F: internal_glmerWrkIter (packages/tests-vg/lme4/src/external.cpp:290) ==3533511== by 0x247B286F: pwrssUpdate (packages/tests-vg/lme4/src/external.cpp:330) ==3533511== by 0x247B8E6C: glmerLaplace (packages/tests-vg/lme4/src/external.cpp:386) ==3533511== by 0x4A91E9: R_doDotCall (svn/R-devel/src/main/dotcode.c:770) ==3533511== by 0x4E4283: bcEval_loop (svn/R-devel/src/main/eval.c:8700) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3533511== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3533511== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3533511== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3533511== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3533511== Address 0x25c9b070 is 48 bytes inside a block of size 41,648 free'd ==3533511== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3533511== by 0x5354C5: ReleaseLargeFreeVectors (svn/R-devel/src/main/memory.c:1167) ==3533511== by 0x5354C5: RunGenCollect (svn/R-devel/src/main/memory.c:1951) ==3533511== by 0x5354C5: R_gc_internal (svn/R-devel/src/main/memory.c:3237) ==3533511== by 0x53830B: CONS_NR (svn/R-devel/src/main/memory.c:2519) ==3533511== by 0x52D9A2: Rf_matchArgs_NR (svn/R-devel/src/main/match.c:196) ==3533511== by 0x52E1B8: Rf_matchArgs_RC (svn/R-devel/src/main/match.c:392) ==3533511== by 0x4D7080: make_applyClosure_env (svn/R-devel/src/main/eval.c:2261) ==3533511== by 0x4F7251: applyClosure_core (svn/R-devel/src/main/eval.c:2304) ==3533511== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3533511== by 0x4F7D61: do_if (svn/R-devel/src/main/eval.c:2709) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== by 0x4F80E4: do_begin (svn/R-devel/src/main/eval.c:3001) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== Block was alloc'd at ==3533511== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3533511== by 0x539581: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2894) ==3533511== by 0x44084B: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3533511== by 0x44084B: Rf_allocMatrix (svn/R-devel/src/main/array.c:236) ==3533511== by 0x162E0DA3: modelmatrix (svn/R-devel/src/library/stats/src/model.c:676) ==3533511== by 0x4A76CE: do_External (svn/R-devel/src/main/dotcode.c:573) ==3533511== by 0x4E63CC: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3533511== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3533511== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3533511== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3533511== by 0x4F7D21: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x53FD2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3533511== ==3533511== Invalid read of size 16 ==3533511== at 0x247D3204: ploadu (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:603) ==3533511== by 0x247D3204: ploadt (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:969) ==3533511== by 0x247D3204: load (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/BlasUtil.h:203) ==3533511== by 0x247D3204: Eigen::internal::general_matrix_vector_product, 0, false, double, Eigen::internal::const_blas_data_mapper, false, 0>::run(long, long, Eigen::internal::const_blas_data_mapper const&, Eigen::internal::const_blas_data_mapper const&, double*, long, double) [clone .isra.0] (R-devel/site-library/RcppEigen/include/Eigen/src/Core/products/GeneralMatrixVector.h:177) ==3533511== by 0x247E7D5B: run >, Eigen::Matrix, Eigen::Matrix > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GeneralProduct.h:253) ==3533511== by 0x247E7D5B: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:388) ==3533511== by 0x247E7D5B: void Eigen::internal::generic_product_impl, 0, Eigen::Stride<0, 0> >, Eigen::Matrix, Eigen::DenseShape, Eigen::DenseShape, 7>::scaleAndAddTo >(Eigen::Matrix&, Eigen::Map, 0, Eigen::Stride<0, 0> > const&, Eigen::Matrix const&, double const&) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:376) ==3533511== by 0x247DD3BE: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:361) ==3533511== by 0x247DD3BE: evalTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:349) ==3533511== by 0x247DD3BE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:148) ==3533511== by 0x247DD3BE: call_assignment_no_alias, Eigen::Product >, Eigen::Matrix, 0>, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3533511== by 0x247DD3BE: run, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:223) ==3533511== by 0x247DD3BE: call_assignment_no_alias, Eigen::CwiseBinaryOp, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3533511== by 0x247DD3BE: _set_noalias, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797) ==3533511== by 0x247DD3BE: PlainObjectBase, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:594) ==3533511== by 0x247DD3BE: Matrix, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:423) ==3533511== by 0x247DD3BE: lme4::merPredD::linPred(double const&) const (packages/tests-vg/lme4/src/predModule.cpp:95) ==3533511== by 0x247B286F: internal_glmerWrkIter (packages/tests-vg/lme4/src/external.cpp:290) ==3533511== by 0x247B286F: pwrssUpdate (packages/tests-vg/lme4/src/external.cpp:330) ==3533511== by 0x247B8E6C: glmerLaplace (packages/tests-vg/lme4/src/external.cpp:386) ==3533511== by 0x4A91E9: R_doDotCall (svn/R-devel/src/main/dotcode.c:770) ==3533511== by 0x4E4283: bcEval_loop (svn/R-devel/src/main/eval.c:8700) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3533511== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3533511== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3533511== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3533511== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3533511== Address 0x25c9b080 is 64 bytes inside a block of size 41,648 free'd ==3533511== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3533511== by 0x5354C5: ReleaseLargeFreeVectors (svn/R-devel/src/main/memory.c:1167) ==3533511== by 0x5354C5: RunGenCollect (svn/R-devel/src/main/memory.c:1951) ==3533511== by 0x5354C5: R_gc_internal (svn/R-devel/src/main/memory.c:3237) ==3533511== by 0x53830B: CONS_NR (svn/R-devel/src/main/memory.c:2519) ==3533511== by 0x52D9A2: Rf_matchArgs_NR (svn/R-devel/src/main/match.c:196) ==3533511== by 0x52E1B8: Rf_matchArgs_RC (svn/R-devel/src/main/match.c:392) ==3533511== by 0x4D7080: make_applyClosure_env (svn/R-devel/src/main/eval.c:2261) ==3533511== by 0x4F7251: applyClosure_core (svn/R-devel/src/main/eval.c:2304) ==3533511== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3533511== by 0x4F7D61: do_if (svn/R-devel/src/main/eval.c:2709) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== by 0x4F80E4: do_begin (svn/R-devel/src/main/eval.c:3001) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== Block was alloc'd at ==3533511== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3533511== by 0x539581: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2894) ==3533511== by 0x44084B: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3533511== by 0x44084B: Rf_allocMatrix (svn/R-devel/src/main/array.c:236) ==3533511== by 0x162E0DA3: modelmatrix (svn/R-devel/src/library/stats/src/model.c:676) ==3533511== by 0x4A76CE: do_External (svn/R-devel/src/main/dotcode.c:573) ==3533511== by 0x4E63CC: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3533511== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3533511== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3533511== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3533511== by 0x4F7D21: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x53FD2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3533511== ==3533511== Invalid read of size 16 ==3533511== at 0x247D3211: ploadu (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:603) ==3533511== by 0x247D3211: ploadt (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:969) ==3533511== by 0x247D3211: load (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/BlasUtil.h:203) ==3533511== by 0x247D3211: Eigen::internal::general_matrix_vector_product, 0, false, double, Eigen::internal::const_blas_data_mapper, false, 0>::run(long, long, Eigen::internal::const_blas_data_mapper const&, Eigen::internal::const_blas_data_mapper const&, double*, long, double) [clone .isra.0] (R-devel/site-library/RcppEigen/include/Eigen/src/Core/products/GeneralMatrixVector.h:177) ==3533511== by 0x247E7D5B: run >, Eigen::Matrix, Eigen::Matrix > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GeneralProduct.h:253) ==3533511== by 0x247E7D5B: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:388) ==3533511== by 0x247E7D5B: void Eigen::internal::generic_product_impl, 0, Eigen::Stride<0, 0> >, Eigen::Matrix, Eigen::DenseShape, Eigen::DenseShape, 7>::scaleAndAddTo >(Eigen::Matrix&, Eigen::Map, 0, Eigen::Stride<0, 0> > const&, Eigen::Matrix const&, double const&) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:376) ==3533511== by 0x247DD3BE: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:361) ==3533511== by 0x247DD3BE: evalTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:349) ==3533511== by 0x247DD3BE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:148) ==3533511== by 0x247DD3BE: call_assignment_no_alias, Eigen::Product >, Eigen::Matrix, 0>, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3533511== by 0x247DD3BE: run, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:223) ==3533511== by 0x247DD3BE: call_assignment_no_alias, Eigen::CwiseBinaryOp, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3533511== by 0x247DD3BE: _set_noalias, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797) ==3533511== by 0x247DD3BE: PlainObjectBase, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:594) ==3533511== by 0x247DD3BE: Matrix, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:423) ==3533511== by 0x247DD3BE: lme4::merPredD::linPred(double const&) const (packages/tests-vg/lme4/src/predModule.cpp:95) ==3533511== by 0x247B286F: internal_glmerWrkIter (packages/tests-vg/lme4/src/external.cpp:290) ==3533511== by 0x247B286F: pwrssUpdate (packages/tests-vg/lme4/src/external.cpp:330) ==3533511== by 0x247B8E6C: glmerLaplace (packages/tests-vg/lme4/src/external.cpp:386) ==3533511== by 0x4A91E9: R_doDotCall (svn/R-devel/src/main/dotcode.c:770) ==3533511== by 0x4E4283: bcEval_loop (svn/R-devel/src/main/eval.c:8700) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3533511== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3533511== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3533511== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3533511== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3533511== Address 0x25c9b090 is 80 bytes inside a block of size 41,648 free'd ==3533511== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3533511== by 0x5354C5: ReleaseLargeFreeVectors (svn/R-devel/src/main/memory.c:1167) ==3533511== by 0x5354C5: RunGenCollect (svn/R-devel/src/main/memory.c:1951) ==3533511== by 0x5354C5: R_gc_internal (svn/R-devel/src/main/memory.c:3237) ==3533511== by 0x53830B: CONS_NR (svn/R-devel/src/main/memory.c:2519) ==3533511== by 0x52D9A2: Rf_matchArgs_NR (svn/R-devel/src/main/match.c:196) ==3533511== by 0x52E1B8: Rf_matchArgs_RC (svn/R-devel/src/main/match.c:392) ==3533511== by 0x4D7080: make_applyClosure_env (svn/R-devel/src/main/eval.c:2261) ==3533511== by 0x4F7251: applyClosure_core (svn/R-devel/src/main/eval.c:2304) ==3533511== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3533511== by 0x4F7D61: do_if (svn/R-devel/src/main/eval.c:2709) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== by 0x4F80E4: do_begin (svn/R-devel/src/main/eval.c:3001) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== Block was alloc'd at ==3533511== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3533511== by 0x539581: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2894) ==3533511== by 0x44084B: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3533511== by 0x44084B: Rf_allocMatrix (svn/R-devel/src/main/array.c:236) ==3533511== by 0x162E0DA3: modelmatrix (svn/R-devel/src/library/stats/src/model.c:676) ==3533511== by 0x4A76CE: do_External (svn/R-devel/src/main/dotcode.c:573) ==3533511== by 0x4E63CC: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3533511== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3533511== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3533511== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3533511== by 0x4F7D21: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x53FD2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3533511== ==3533511== Invalid read of size 16 ==3533511== at 0x247D321E: pmul (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:237) ==3533511== by 0x247D321E: pmadd (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:959) ==3533511== by 0x247D321E: pmadd (R-devel/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:95) ==3533511== by 0x247D321E: Eigen::internal::general_matrix_vector_product, 0, false, double, Eigen::internal::const_blas_data_mapper, false, 0>::run(long, long, Eigen::internal::const_blas_data_mapper const&, Eigen::internal::const_blas_data_mapper const&, double*, long, double) [clone .isra.0] (R-devel/site-library/RcppEigen/include/Eigen/src/Core/products/GeneralMatrixVector.h:177) ==3533511== by 0x247E7D5B: run >, Eigen::Matrix, Eigen::Matrix > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GeneralProduct.h:253) ==3533511== by 0x247E7D5B: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:388) ==3533511== by 0x247E7D5B: void Eigen::internal::generic_product_impl, 0, Eigen::Stride<0, 0> >, Eigen::Matrix, Eigen::DenseShape, Eigen::DenseShape, 7>::scaleAndAddTo >(Eigen::Matrix&, Eigen::Map, 0, Eigen::Stride<0, 0> > const&, Eigen::Matrix const&, double const&) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:376) ==3533511== by 0x247DD3BE: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:361) ==3533511== by 0x247DD3BE: evalTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:349) ==3533511== by 0x247DD3BE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:148) ==3533511== by 0x247DD3BE: call_assignment_no_alias, Eigen::Product >, Eigen::Matrix, 0>, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3533511== by 0x247DD3BE: run, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:223) ==3533511== by 0x247DD3BE: call_assignment_no_alias, Eigen::CwiseBinaryOp, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3533511== by 0x247DD3BE: _set_noalias, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797) ==3533511== by 0x247DD3BE: PlainObjectBase, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:594) ==3533511== by 0x247DD3BE: Matrix, const Eigen::Product >, Eigen::Matrix, 0>, const Eigen::Product > >, Eigen::Matrix, 0> > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:423) ==3533511== by 0x247DD3BE: lme4::merPredD::linPred(double const&) const (packages/tests-vg/lme4/src/predModule.cpp:95) ==3533511== by 0x247B286F: internal_glmerWrkIter (packages/tests-vg/lme4/src/external.cpp:290) ==3533511== by 0x247B286F: pwrssUpdate (packages/tests-vg/lme4/src/external.cpp:330) ==3533511== by 0x247B8E6C: glmerLaplace (packages/tests-vg/lme4/src/external.cpp:386) ==3533511== by 0x4A91E9: R_doDotCall (svn/R-devel/src/main/dotcode.c:770) ==3533511== by 0x4E4283: bcEval_loop (svn/R-devel/src/main/eval.c:8700) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3533511== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3533511== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3533511== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3533511== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3533511== Address 0x25c9b0a0 is 96 bytes inside a block of size 41,648 free'd ==3533511== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3533511== by 0x5354C5: ReleaseLargeFreeVectors (svn/R-devel/src/main/memory.c:1167) ==3533511== by 0x5354C5: RunGenCollect (svn/R-devel/src/main/memory.c:1951) ==3533511== by 0x5354C5: R_gc_internal (svn/R-devel/src/main/memory.c:3237) ==3533511== by 0x53830B: CONS_NR (svn/R-devel/src/main/memory.c:2519) ==3533511== by 0x52D9A2: Rf_matchArgs_NR (svn/R-devel/src/main/match.c:196) ==3533511== by 0x52E1B8: Rf_matchArgs_RC (svn/R-devel/src/main/match.c:392) ==3533511== by 0x4D7080: make_applyClosure_env (svn/R-devel/src/main/eval.c:2261) ==3533511== by 0x4F7251: applyClosure_core (svn/R-devel/src/main/eval.c:2304) ==3533511== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3533511== by 0x4F7D61: do_if (svn/R-devel/src/main/eval.c:2709) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== by 0x4F80E4: do_begin (svn/R-devel/src/main/eval.c:3001) ==3533511== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3533511== Block was alloc'd at ==3533511== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3533511== by 0x539581: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2894) ==3533511== by 0x44084B: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3533511== by 0x44084B: Rf_allocMatrix (svn/R-devel/src/main/array.c:236) ==3533511== by 0x162E0DA3: modelmatrix (svn/R-devel/src/library/stats/src/model.c:676) ==3533511== by 0x4A76CE: do_External (svn/R-devel/src/main/dotcode.c:573) ==3533511== by 0x4E63CC: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3533511== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3533511== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3533511== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3533511== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3533511== by 0x4F7D21: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3533511== by 0x53FD2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3533511== boundary (singular) fit: see help('isSingular') > > proc.time() user system elapsed 310.268 1.873 311.575 ==3533511== ==3533511== HEAP SUMMARY: ==3533511== in use at exit: 219,976,337 bytes in 44,510 blocks ==3533511== total heap usage: 399,640 allocs, 355,130 frees, 3,684,542,093 bytes allocated ==3533511== ==3533511== LEAK SUMMARY: ==3533511== definitely lost: 0 bytes in 0 blocks ==3533511== indirectly lost: 0 bytes in 0 blocks ==3533511== possibly lost: 0 bytes in 0 blocks ==3533511== still reachable: 219,976,337 bytes in 44,510 blocks ==3533511== suppressed: 0 bytes in 0 blocks ==3533511== Reachable blocks (those to which a pointer was found) are not shown. ==3533511== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3533511== ==3533511== For lists of detected and suppressed errors, rerun with: -s ==3533511== ERROR SUMMARY: 3627000 errors from 5 contexts (suppressed: 0 from 0)