==3521979== Memcheck, a memory error detector ==3521979== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. ==3521979== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info ==3521979== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R -f glmmExt.R --restore --save --no-readline --vanilla ==3521979== 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. > ## 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")) ==3521979== Invalid read of size 8 ==3521979== at 0x247DA545: coeff (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:925) ==3521979== by 0x247DA545: assignCoeff (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654) ==3521979== by 0x247DA545: assignCoeffByOuterInner (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:668) ==3521979== by 0x247DA545: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:347) ==3521979== 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) ==3521979== by 0x247DA545: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3521979== 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) ==3521979== 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) ==3521979== by 0x247DA545: call_assignment >, Eigen::Product > >, Eigen::Map >, 1> > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3521979== by 0x247DA545: operator= > >, Eigen::Map >, 1> > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Assign.h:66) ==3521979== by 0x247DA545: lme4::merPredD::updateXwts(Eigen::Array const&) (packages/tests-vg/lme4/src/predModule.cpp:221) ==3521979== by 0x247B2A2F: internal_glmerWrkIter (packages/tests-vg/lme4/src/external.cpp:274) ==3521979== by 0x247B2A2F: pwrssUpdate (packages/tests-vg/lme4/src/external.cpp:330) ==3521979== by 0x247B8E6C: glmerLaplace (packages/tests-vg/lme4/src/external.cpp:386) ==3521979== by 0x4A91E9: R_doDotCall (svn/R-devel/src/main/dotcode.c:770) ==3521979== by 0x4E4283: bcEval_loop (svn/R-devel/src/main/eval.c:8700) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3521979== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3521979== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3521979== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3521979== by 0x4F96BC: do_set (svn/R-devel/src/main/eval.c:3585) ==3521979== by 0x4F49B2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3521979== Address 0x25297f70 is 48 bytes inside a block of size 41,648 free'd ==3521979== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3521979== by 0x5354C5: ReleaseLargeFreeVectors (svn/R-devel/src/main/memory.c:1167) ==3521979== by 0x5354C5: RunGenCollect (svn/R-devel/src/main/memory.c:1951) ==3521979== by 0x5354C5: R_gc_internal (svn/R-devel/src/main/memory.c:3237) ==3521979== by 0x537ADE: Rf_cons (svn/R-devel/src/main/memory.c:2488) ==3521979== by 0x4B1FB7: duplicate_list (svn/R-devel/src/main/duplicate.c:267) ==3521979== by 0x4B18D2: duplicate1 (svn/R-devel/src/main/duplicate.c:320) ==3521979== by 0x4E8FCD: bcEval_loop (svn/R-devel/src/main/eval.c:8317) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F4E56: forcePromise.part.0 (svn/R-devel/src/main/eval.c:976) ==3521979== by 0x4F4818: forcePromise (svn/R-devel/src/main/eval.c:956) ==3521979== by 0x4F4818: Rf_eval (svn/R-devel/src/main/eval.c:1185) ==3521979== by 0x5B9112: R_DispatchOrEvalSP (svn/R-devel/src/main/subset.c:657) ==3521979== by 0x5BD795: do_subset (svn/R-devel/src/main/subset.c:691) ==3521979== Block was alloc'd at ==3521979== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3521979== by 0x539581: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2894) ==3521979== by 0x44084B: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3521979== by 0x44084B: Rf_allocMatrix (svn/R-devel/src/main/array.c:236) ==3521979== by 0x162E0DA3: modelmatrix (svn/R-devel/src/library/stats/src/model.c:676) ==3521979== by 0x4A76CE: do_External (svn/R-devel/src/main/dotcode.c:573) ==3521979== by 0x4E63CC: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3521979== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3521979== by 0x4F7D21: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3521979== by 0x53FD2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3521979== ==3521979== Invalid read of size 16 ==3521979== at 0x247D31F4: ploadu (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:603) ==3521979== by 0x247D31F4: ploadt (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:969) ==3521979== by 0x247D31F4: load (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/BlasUtil.h:203) ==3521979== 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) ==3521979== by 0x247E7D5B: run >, Eigen::Matrix, Eigen::Matrix > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GeneralProduct.h:253) ==3521979== by 0x247E7D5B: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:388) ==3521979== 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) ==3521979== by 0x247DD3BE: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:361) ==3521979== by 0x247DD3BE: evalTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:349) ==3521979== by 0x247DD3BE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:148) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== by 0x247DD3BE: lme4::merPredD::linPred(double const&) const (packages/tests-vg/lme4/src/predModule.cpp:95) ==3521979== by 0x247B286F: internal_glmerWrkIter (packages/tests-vg/lme4/src/external.cpp:290) ==3521979== by 0x247B286F: pwrssUpdate (packages/tests-vg/lme4/src/external.cpp:330) ==3521979== by 0x247B8E6C: glmerLaplace (packages/tests-vg/lme4/src/external.cpp:386) ==3521979== by 0x4A91E9: R_doDotCall (svn/R-devel/src/main/dotcode.c:770) ==3521979== by 0x4E4283: bcEval_loop (svn/R-devel/src/main/eval.c:8700) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3521979== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3521979== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3521979== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3521979== Address 0x25297f70 is 48 bytes inside a block of size 41,648 free'd ==3521979== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3521979== by 0x5354C5: ReleaseLargeFreeVectors (svn/R-devel/src/main/memory.c:1167) ==3521979== by 0x5354C5: RunGenCollect (svn/R-devel/src/main/memory.c:1951) ==3521979== by 0x5354C5: R_gc_internal (svn/R-devel/src/main/memory.c:3237) ==3521979== by 0x537ADE: Rf_cons (svn/R-devel/src/main/memory.c:2488) ==3521979== by 0x4B1FB7: duplicate_list (svn/R-devel/src/main/duplicate.c:267) ==3521979== by 0x4B18D2: duplicate1 (svn/R-devel/src/main/duplicate.c:320) ==3521979== by 0x4E8FCD: bcEval_loop (svn/R-devel/src/main/eval.c:8317) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F4E56: forcePromise.part.0 (svn/R-devel/src/main/eval.c:976) ==3521979== by 0x4F4818: forcePromise (svn/R-devel/src/main/eval.c:956) ==3521979== by 0x4F4818: Rf_eval (svn/R-devel/src/main/eval.c:1185) ==3521979== by 0x5B9112: R_DispatchOrEvalSP (svn/R-devel/src/main/subset.c:657) ==3521979== by 0x5BD795: do_subset (svn/R-devel/src/main/subset.c:691) ==3521979== Block was alloc'd at ==3521979== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3521979== by 0x539581: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2894) ==3521979== by 0x44084B: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3521979== by 0x44084B: Rf_allocMatrix (svn/R-devel/src/main/array.c:236) ==3521979== by 0x162E0DA3: modelmatrix (svn/R-devel/src/library/stats/src/model.c:676) ==3521979== by 0x4A76CE: do_External (svn/R-devel/src/main/dotcode.c:573) ==3521979== by 0x4E63CC: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3521979== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3521979== by 0x4F7D21: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3521979== by 0x53FD2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3521979== ==3521979== Invalid read of size 16 ==3521979== at 0x247D3204: ploadu (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:603) ==3521979== by 0x247D3204: ploadt (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:969) ==3521979== by 0x247D3204: load (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/BlasUtil.h:203) ==3521979== 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) ==3521979== by 0x247E7D5B: run >, Eigen::Matrix, Eigen::Matrix > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GeneralProduct.h:253) ==3521979== by 0x247E7D5B: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:388) ==3521979== 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) ==3521979== by 0x247DD3BE: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:361) ==3521979== by 0x247DD3BE: evalTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:349) ==3521979== by 0x247DD3BE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:148) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== by 0x247DD3BE: lme4::merPredD::linPred(double const&) const (packages/tests-vg/lme4/src/predModule.cpp:95) ==3521979== by 0x247B286F: internal_glmerWrkIter (packages/tests-vg/lme4/src/external.cpp:290) ==3521979== by 0x247B286F: pwrssUpdate (packages/tests-vg/lme4/src/external.cpp:330) ==3521979== by 0x247B8E6C: glmerLaplace (packages/tests-vg/lme4/src/external.cpp:386) ==3521979== by 0x4A91E9: R_doDotCall (svn/R-devel/src/main/dotcode.c:770) ==3521979== by 0x4E4283: bcEval_loop (svn/R-devel/src/main/eval.c:8700) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3521979== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3521979== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3521979== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3521979== Address 0x25297f80 is 64 bytes inside a block of size 41,648 free'd ==3521979== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3521979== by 0x5354C5: ReleaseLargeFreeVectors (svn/R-devel/src/main/memory.c:1167) ==3521979== by 0x5354C5: RunGenCollect (svn/R-devel/src/main/memory.c:1951) ==3521979== by 0x5354C5: R_gc_internal (svn/R-devel/src/main/memory.c:3237) ==3521979== by 0x537ADE: Rf_cons (svn/R-devel/src/main/memory.c:2488) ==3521979== by 0x4B1FB7: duplicate_list (svn/R-devel/src/main/duplicate.c:267) ==3521979== by 0x4B18D2: duplicate1 (svn/R-devel/src/main/duplicate.c:320) ==3521979== by 0x4E8FCD: bcEval_loop (svn/R-devel/src/main/eval.c:8317) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F4E56: forcePromise.part.0 (svn/R-devel/src/main/eval.c:976) ==3521979== by 0x4F4818: forcePromise (svn/R-devel/src/main/eval.c:956) ==3521979== by 0x4F4818: Rf_eval (svn/R-devel/src/main/eval.c:1185) ==3521979== by 0x5B9112: R_DispatchOrEvalSP (svn/R-devel/src/main/subset.c:657) ==3521979== by 0x5BD795: do_subset (svn/R-devel/src/main/subset.c:691) ==3521979== Block was alloc'd at ==3521979== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3521979== by 0x539581: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2894) ==3521979== by 0x44084B: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3521979== by 0x44084B: Rf_allocMatrix (svn/R-devel/src/main/array.c:236) ==3521979== by 0x162E0DA3: modelmatrix (svn/R-devel/src/library/stats/src/model.c:676) ==3521979== by 0x4A76CE: do_External (svn/R-devel/src/main/dotcode.c:573) ==3521979== by 0x4E63CC: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3521979== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3521979== by 0x4F7D21: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3521979== by 0x53FD2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3521979== ==3521979== Invalid read of size 16 ==3521979== at 0x247D3211: ploadu (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:603) ==3521979== by 0x247D3211: ploadt (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:969) ==3521979== by 0x247D3211: load (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/BlasUtil.h:203) ==3521979== 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) ==3521979== by 0x247E7D5B: run >, Eigen::Matrix, Eigen::Matrix > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GeneralProduct.h:253) ==3521979== by 0x247E7D5B: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:388) ==3521979== 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) ==3521979== by 0x247DD3BE: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:361) ==3521979== by 0x247DD3BE: evalTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:349) ==3521979== by 0x247DD3BE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:148) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== by 0x247DD3BE: lme4::merPredD::linPred(double const&) const (packages/tests-vg/lme4/src/predModule.cpp:95) ==3521979== by 0x247B286F: internal_glmerWrkIter (packages/tests-vg/lme4/src/external.cpp:290) ==3521979== by 0x247B286F: pwrssUpdate (packages/tests-vg/lme4/src/external.cpp:330) ==3521979== by 0x247B8E6C: glmerLaplace (packages/tests-vg/lme4/src/external.cpp:386) ==3521979== by 0x4A91E9: R_doDotCall (svn/R-devel/src/main/dotcode.c:770) ==3521979== by 0x4E4283: bcEval_loop (svn/R-devel/src/main/eval.c:8700) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3521979== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3521979== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3521979== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3521979== Address 0x25297f90 is 80 bytes inside a block of size 41,648 free'd ==3521979== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3521979== by 0x5354C5: ReleaseLargeFreeVectors (svn/R-devel/src/main/memory.c:1167) ==3521979== by 0x5354C5: RunGenCollect (svn/R-devel/src/main/memory.c:1951) ==3521979== by 0x5354C5: R_gc_internal (svn/R-devel/src/main/memory.c:3237) ==3521979== by 0x537ADE: Rf_cons (svn/R-devel/src/main/memory.c:2488) ==3521979== by 0x4B1FB7: duplicate_list (svn/R-devel/src/main/duplicate.c:267) ==3521979== by 0x4B18D2: duplicate1 (svn/R-devel/src/main/duplicate.c:320) ==3521979== by 0x4E8FCD: bcEval_loop (svn/R-devel/src/main/eval.c:8317) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F4E56: forcePromise.part.0 (svn/R-devel/src/main/eval.c:976) ==3521979== by 0x4F4818: forcePromise (svn/R-devel/src/main/eval.c:956) ==3521979== by 0x4F4818: Rf_eval (svn/R-devel/src/main/eval.c:1185) ==3521979== by 0x5B9112: R_DispatchOrEvalSP (svn/R-devel/src/main/subset.c:657) ==3521979== by 0x5BD795: do_subset (svn/R-devel/src/main/subset.c:691) ==3521979== Block was alloc'd at ==3521979== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3521979== by 0x539581: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2894) ==3521979== by 0x44084B: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3521979== by 0x44084B: Rf_allocMatrix (svn/R-devel/src/main/array.c:236) ==3521979== by 0x162E0DA3: modelmatrix (svn/R-devel/src/library/stats/src/model.c:676) ==3521979== by 0x4A76CE: do_External (svn/R-devel/src/main/dotcode.c:573) ==3521979== by 0x4E63CC: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3521979== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3521979== by 0x4F7D21: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3521979== by 0x53FD2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3521979== ==3521979== Invalid read of size 16 ==3521979== at 0x247D321E: pmul (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:237) ==3521979== by 0x247D321E: pmadd (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:959) ==3521979== by 0x247D321E: pmadd (R-devel/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:95) ==3521979== 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) ==3521979== by 0x247E7D5B: run >, Eigen::Matrix, Eigen::Matrix > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/GeneralProduct.h:253) ==3521979== by 0x247E7D5B: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:388) ==3521979== 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) ==3521979== by 0x247DD3BE: scaleAndAddTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:361) ==3521979== by 0x247DD3BE: evalTo > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:349) ==3521979== by 0x247DD3BE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:148) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== 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) ==3521979== by 0x247DD3BE: lme4::merPredD::linPred(double const&) const (packages/tests-vg/lme4/src/predModule.cpp:95) ==3521979== by 0x247B286F: internal_glmerWrkIter (packages/tests-vg/lme4/src/external.cpp:290) ==3521979== by 0x247B286F: pwrssUpdate (packages/tests-vg/lme4/src/external.cpp:330) ==3521979== by 0x247B8E6C: glmerLaplace (packages/tests-vg/lme4/src/external.cpp:386) ==3521979== by 0x4A91E9: R_doDotCall (svn/R-devel/src/main/dotcode.c:770) ==3521979== by 0x4E4283: bcEval_loop (svn/R-devel/src/main/eval.c:8700) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3521979== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3521979== by 0x4F475A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3521979== by 0x4F475A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3521979== Address 0x25297fa0 is 96 bytes inside a block of size 41,648 free'd ==3521979== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3521979== by 0x5354C5: ReleaseLargeFreeVectors (svn/R-devel/src/main/memory.c:1167) ==3521979== by 0x5354C5: RunGenCollect (svn/R-devel/src/main/memory.c:1951) ==3521979== by 0x5354C5: R_gc_internal (svn/R-devel/src/main/memory.c:3237) ==3521979== by 0x537ADE: Rf_cons (svn/R-devel/src/main/memory.c:2488) ==3521979== by 0x4B1FB7: duplicate_list (svn/R-devel/src/main/duplicate.c:267) ==3521979== by 0x4B18D2: duplicate1 (svn/R-devel/src/main/duplicate.c:320) ==3521979== by 0x4E8FCD: bcEval_loop (svn/R-devel/src/main/eval.c:8317) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F4E56: forcePromise.part.0 (svn/R-devel/src/main/eval.c:976) ==3521979== by 0x4F4818: forcePromise (svn/R-devel/src/main/eval.c:956) ==3521979== by 0x4F4818: Rf_eval (svn/R-devel/src/main/eval.c:1185) ==3521979== by 0x5B9112: R_DispatchOrEvalSP (svn/R-devel/src/main/subset.c:657) ==3521979== by 0x5BD795: do_subset (svn/R-devel/src/main/subset.c:691) ==3521979== Block was alloc'd at ==3521979== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3521979== by 0x539581: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2894) ==3521979== by 0x44084B: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3521979== by 0x44084B: Rf_allocMatrix (svn/R-devel/src/main/array.c:236) ==3521979== by 0x162E0DA3: modelmatrix (svn/R-devel/src/library/stats/src/model.c:676) ==3521979== by 0x4A76CE: do_External (svn/R-devel/src/main/dotcode.c:573) ==3521979== by 0x4E63CC: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7533) ==3521979== by 0x4F4317: bcEval (svn/R-devel/src/main/eval.c:7518) ==3521979== by 0x4F464A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3521979== by 0x4F65DD: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3521979== by 0x4F729F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3521979== by 0x4F7D21: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3521979== by 0x53FD2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3521979== > gBc1 <- glmer(y ~ 1 + (1 | block), data = dBc, family = binomial(link = "cloglog")) > gBc2 <- glmer(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 = 0.005)) > stopifnot(all.equal(unname(unlist(VarCorr(gBc2))), c(glmmadmbfit$VarCorr$block), + tolerance = 0.02)) > gBi1 <- glmer(y ~ 1 + (1 | block), data = dBi, family = binomial(link = "identity")) > gBi2 <- glmer(y ~ x + (1 | block), data = dBi, family = binomial(link = "identity")) Warning messages: 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : Model is nearly unidentifiable: very large eigenvalue - Rescale variables? 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : Model failed to converge with max|grad| = 0.0164641 (tol = 0.002, component 1) See ?lme4::convergence and ?lme4::troubleshooting. > > proc.time() user system elapsed 327.350 2.009 328.946 ==3521979== ==3521979== HEAP SUMMARY: ==3521979== in use at exit: 231,014,659 bytes in 44,345 blocks ==3521979== total heap usage: 544,677 allocs, 500,332 frees, 4,883,037,288 bytes allocated ==3521979== ==3521979== LEAK SUMMARY: ==3521979== definitely lost: 0 bytes in 0 blocks ==3521979== indirectly lost: 0 bytes in 0 blocks ==3521979== possibly lost: 0 bytes in 0 blocks ==3521979== still reachable: 231,014,659 bytes in 44,345 blocks ==3521979== suppressed: 0 bytes in 0 blocks ==3521979== Reachable blocks (those to which a pointer was found) are not shown. ==3521979== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3521979== ==3521979== For lists of detected and suppressed errors, rerun with: -s ==3521979== ERROR SUMMARY: 2368606 errors from 5 contexts (suppressed: 0 from 0)