* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/nlme.Rcheck’ * using R Under development (unstable) (2026-07-18 r90269) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-07-19 00:53:04 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘nlme/DESCRIPTION’ ... OK * this is package ‘nlme’ version ‘3.1-170’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘nlme’ can be installed ... [18s/19s] OK * used C compiler: ‘gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’ * used Fortran compiler: ‘GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’ * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [34s/35s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking usage of KIND in Fortran files ... OK * checking examples ... [30s/31s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Processing ‘extras.Rin’ Running ‘anova.gls.R’ Running ‘augPred_lab.R’ [11s/12s] Running ‘augPredmissing.R’ Running ‘coef.R’ Comparing ‘coef.Rout’ to ‘coef.Rout.save’ ... OK Running ‘contrMat.R’ Running ‘corMatrix.R’ Running ‘corStruct.R’ Running ‘data.frame.R’ Running ‘deparse.R’ Running ‘deviance.R’ Running ‘fitted.R’ Running ‘getData.R’ Running ‘getVarCov.R’ Running ‘gls.R’ Running ‘gnls-ch8.R’ Running ‘lmList.R’ Running ‘lme.R’ Running ‘missing.R’ Comparing ‘missing.Rout’ to ‘missing.Rout.save’ ... OK Running ‘nlme.R’ Running ‘nlme2.R’ Running ‘predict.lme.R’ Running ‘scoping.R’ Running ‘sigma-fixed-etc.R’ [10s/10s] Running ‘updateLme.R’ Running ‘varConstProp.R’ Running ‘varFixed.R’ Running ‘varIdent.R’ [37s/41s] ERROR Running the tests in ‘tests/lme.R’ failed. Complete output: > library(nlme) > > options(digits = 6)# <==> less platform dependency in print() output > if(!dev.interactive(orNone=TRUE)) pdf("test_lme.pdf") > > fm1 <- lmList(Oxboys) > fm1 Call: Model: height ~ age | Subject Data: Oxboys Coefficients: (Intercept) age 10 130.262 3.72291 26 137.993 5.58878 25 139.210 4.02408 9 138.137 6.00906 2 142.858 5.44018 6 146.791 3.96317 7 146.128 4.99005 17 142.978 8.61178 16 147.545 4.54520 15 144.276 7.12426 8 148.293 6.46471 20 151.471 4.37447 1 148.120 7.17815 18 151.180 5.95779 5 151.429 6.24613 23 151.065 7.18512 11 150.047 8.50608 21 150.521 7.49779 3 155.651 4.77467 24 153.140 6.76470 22 154.567 8.08751 12 156.811 7.01547 13 156.071 8.49381 14 159.474 8.67089 19 164.576 9.06562 4 165.072 9.36056 Degrees of freedom: 234 total; 182 residual Residual standard error: 0.659888 > fm2 <- lme(fm1) > fm2 Linear mixed-effects model fit by REML Data: Oxboys Log-restricted-likelihood: -362.045 Fixed: height ~ age (Intercept) age 149.37175 6.52547 Random effects: Formula: ~age | Subject Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 8.081077 (Intr) age 1.680717 0.641 Residual 0.659889 Number of Observations: 234 Number of Groups: 26 > vc2 <- VarCorr(fm2) > stopifnot( + all.equal(fixef(fm2), c("(Intercept)" = 149.371753, + age = 6.52546866), tol=1e-8), + all.equal(as.numeric(vc2[,"StdDev"]), + c(8.081077, 1.680717, 0.659889), tol=4e-7)) > > # bug report from Arne.Mueller@sanofi-aventis.com > mod <- distance ~ age + Sex > fm3 <- lme(mod, Orthodont, random = ~ 1) > pm3 <- predict(fm3, Orthodont) > stopifnot(all.equal(mean(pm3), 24.023148148), + all.equal( sd(pm3), 2.4802195115), + all.equal(quantile(pm3), c("0%" = 17.0817792, "25%" = 22.3481813, + "50%" = 23.9271016, "75%" = 25.5740014, + "100%"= 30.8662241))) > > > ## bug report and fix from Dimitris Rizopoulos and Spencer Graves: > ## when 'returnObject = TRUE', do not stop() but give warning() on non-convergence: > tools::assertWarning( + fm1 <- lme(distance ~ age, data = Orthodont, + control = lmeControl(msMaxIter = 1, returnObject = TRUE)) + ) > > ## "typo" in 'random=' -- giving 27-dim. vector random effect: > ## PR#17524 B.Tyner: https://bugs.r-project.org/show_bug.cgi?id=17524 > try(lme(distance ~ 1, data=Orthodont, random = ~ Subject)) Error in lme.formula(distance ~ 1, data = Orthodont, random = ~Subject) : fewer observations than random effects in all level 1 groups > tools::assertError(lme(distance ~ age, data=Orthodont, random = ~ Subject)) > ## seg.faults in nlme <= 3.1-137 (2018) because of integer overflow > ## The previous warning is now an *error* (unless new lmeControl(allow.n.lt.q=TRUE)) > > > ## based on bug report on R-help > (p3.1 <- predict(fm3, Orthodont[1,])) M01 25.3924 attr(,"label") [1] "Predicted values (mm)" > # failed in 3.1-88 > stopifnot(all.equal(pm3[1], p3.1, + check.attributes=FALSE, tolerance = 1e-14)) > > ## Intervals failed in a patch proposal (Nov.2015): > (fm4 <- lme(distance ~ age, Orthodont, random = ~ age | Subject)) Linear mixed-effects model fit by REML Data: Orthodont Log-restricted-likelihood: -221.318 Fixed: distance ~ age (Intercept) age 16.761111 0.660185 Random effects: Formula: ~age | Subject Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 2.327034 (Intr) age 0.226428 -0.609 Residual 1.310040 Number of Observations: 108 Number of Groups: 27 > i4 <- intervals(fm4) > ## from dput(signif(i4$reStruct$Subject, 8)) > ## R-devel 2016-01-11; 64-bit : > reSS <- data.frame(lower = c(0.9485605, 0.10250901, -0.93825047), + est. = c(2.3270341, 0.22642779, -0.60933286), + upper = c(5.7087424, 0.50014674, 0.29816857)) > ## R-devel 2016-01-11; 32-bit : > ## reSS <- data.frame(lower = c(0.94962127,0.10262181, -0.93804767), > ## est. = c(2.3270339, 0.22642779, -0.60933284), > ## upper = c(5.7023648, 0.49959695, 0.29662651)) > rownames(reSS) <- rownames(i4$reStruct$Subject) > sm4 <- summary(fm4) > stopifnot( + all.equal(fixef(fm4), + c("(Intercept)" = 16.761111, age = 0.66018519)), + identical(fixef(fm4), sm4$tTable[,"Value"]), + all.equal(sm4$tTable[,"Std.Error"], + c("(Intercept)" = 0.77524603, age = 0.071253264), tol=6e-8), + all.equal(i4$reStruct$Subject[,"est."], reSS[,"est."], tol= 1e-7) + ## (lower, upper) cannot be very accurate for these : ==> tol = *e-4 + ,## "interestingly" 32-bit values changed from 3.2.3 to R-devel(3.3.0): + all.equal(i4$reStruct$Subject[,c(1,3)], reSS[,c(1,3)], tol = .005) + , + all.equal(as.vector(i4$sigma), + ## lower est. upper + c(1.0849772, 1.3100397, 1.5817881), tol=8e-4) + , + all.equal(as.vector(i4$fixed), + as.vector(rbind(c(15.218322, 16.761111, 18.3039), + c(0.51838667, 0.66018519, 0.8019837))), + tol = 1e-6) + ) Error: i4$reStruct$Subject[, "est."] and reSS[, "est."] are not equal: Mean relative difference: 1.05353e-07 Execution halted * checking PDF version of manual ... [14s/15s] OK * checking HTML version of manual ... [11s/11s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-MKL/nlme.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 3:09.27, 169.24 + 9.66