* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/robustbase.Rcheck’ * using R Under development (unstable) (2026-10-30 r90795) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-10-30 08:16:40 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘robustbase/DESCRIPTION’ ... OK * this is package ‘robustbase’ version ‘0.99-7’ * 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 ‘robustbase’ can be installed ... [17s/18s] OK * used C compiler: ‘gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’ * used Fortran compiler: ‘GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’ * checking package directory ... OK * checking ‘build’ 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 loading without being on the library search path ... 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 ... [21s/22s] 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘robustbase-Ex.R’ failed The error most likely occurred in: > ### Name: covMcd > ### Title: Robust Location and Scatter Estimation via MCD > ### Aliases: covMcd print.mcd .MCDcons .MCDcnp2 .MCDcnp2.rew > ### .MCDsingularityMsg .wgtFUN.covMcd > ### Keywords: robust multivariate > > ### ** Examples > > data(hbk) > hbk.x <- data.matrix(hbk[, 1:3]) > set.seed(17) > (cH <- covMcd(hbk.x)) Minimum Covariance Determinant (MCD) estimator approximation. Method: Fast MCD(alpha=0.5 ==> h=39); nsamp = 500; (n,k)mini = (300,5) Call: covMcd(x = hbk.x) Log(Det.): -1.048 Robust Estimate of Location: X1 X2 X3 1.538 1.780 1.687 Robust Estimate of Covariance: X1 X2 X3 X1 1.22689 0.05501 0.1272 X2 0.05501 1.24880 0.1525 X3 0.12717 0.15253 1.1598 > cH0 <- covMcd(hbk.x, nsamp = "deterministic") > with(cH0, stopifnot(quan == 39, + iBest == c(1:4,6), # 5 out of 6 gave the same + identical(raw.weights, mcd.wt), + identical(which(mcd.wt == 0), 1:14), all.equal(crit, -1.045500594135))) Warning in iBest == c(1:4, 6) : longer object length is not a multiple of shorter object length Error in eval(substitute(expr), data, enclos = parent.frame()) : iBest == c(1:4, 6) are not all TRUE Calls: with -> with.default -> eval -> eval -> stopifnot Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘LTS-specials.R’ Running ‘MCD-specials.R’ Comparing ‘MCD-specials.Rout’ to ‘MCD-specials.Rout.save’ ... OK Running ‘MT-tst.R’ Running ‘NAcoef.R’ Comparing ‘NAcoef.Rout’ to ‘NAcoef.Rout.save’ ... OK Running ‘OGK-ex.R’ Comparing ‘OGK-ex.Rout’ to ‘OGK-ex.Rout.save’ ... OK Running ‘Qn-Sn-plots.R’ Running ‘Rsquared.R’ Comparing ‘Rsquared.Rout’ to ‘Rsquared.Rout.save’ ... OK Running ‘binom-ni-small.R’ Comparing ‘binom-ni-small.Rout’ to ‘binom-ni-small.Rout.save’ ... OK Running ‘binom-no-x.R’ Running ‘comedian-tst.R’ Running ‘exact-fit-categorical.R’ Running ‘glmrob-1.R’ Running ‘glmrob-specials.R’ Running ‘huber-etc.R’ Comparing ‘huber-etc.Rout’ to ‘huber-etc.Rout.save’ ... OK Running ‘large-values.R’ Running ‘lmrob-data.R’ Running ‘lmrob-ex12.R’ Running ‘lmrob-methods.R’ Comparing ‘lmrob-methods.Rout’ to ‘lmrob-methods.Rout.save’ ... OK Running ‘lmrob-psifns.R’ Comparing ‘lmrob-psifns.Rout’ to ‘lmrob-psifns.Rout.save’ ... OK Running ‘m-s-estimator.R’ Running ‘mc-etc.R’ Running ‘mc-strict.R’ [10s/10s] Running ‘nlregrob-tst.R’ Running ‘nlrob-tst.R’ Running ‘poisson-ex.R’ Running ‘psi-rho-etc.R’ Comparing ‘psi-rho-etc.Rout’ to ‘psi-rho-etc.Rout.save’ ... OK Running ‘small-sample.R’ Comparing ‘small-sample.Rout’ to ‘small-sample.Rout.save’ ... OK Running ‘subsample.R’ Running ‘tlts.R’ Comparing ‘tlts.Rout’ to ‘tlts.Rout.save’ ... OK Running ‘tmcd.R’ Running ‘weights.R’ Comparing ‘weights.Rout’ to ‘weights.Rout.save’ ... OK Running ‘wgt-himed-xtra.R’ Running ‘wgt-himed.R’ Comparing ‘wgt-himed.Rout’ to ‘wgt-himed.Rout.save’ ... OK [62s/66s] ERROR Running the tests in ‘tests/nlrob-tst.R’ failed. Complete output: > commandArgs() [1] "/data/localhost/ripley/R/MKL/bin/exec/R" [2] "-f" [3] "nlrob-tst.R" [4] "--restore" [5] "--save" [6] "--no-readline" [7] "--vanilla" > library(robustbase) > > ## for now: ---------------------------------------- > if(file.exists(fil <- system.file("xtraR/test-tools.R", package = "robustbase"))) { + source(fil) + } else { + identical3 <- function(x,y,z) identical(x,y) && identical (y,z) + identical4 <- function(a,b,c,d) identical(a,b) && identical3(b,c,d) + assert.EQ <- function(target, current, tol = if(showOnly) 0 else 1e-15, + giveRE = FALSE, showOnly = FALSE, ...) { + ## Purpose: check equality *and* show non-equality + ## ---------------------------------------------------------------------- + ## showOnly: if TRUE, return (and hence typically print) all.equal(...) + T <- isTRUE(ae <- all.equal(target, current, tolerance = tol, ...)) + if(showOnly) return(ae) else if(giveRE && T) { ## don't show if stop() later: + ae0 <- if(tol == 0) ae else all.equal(target, current, tolerance = 0, ...) + if(!isTRUE(ae0)) writeLines(ae0) + } + if(!T) stop("all.equal() |-> ", paste(ae, collapse=sprintf("%-19s","\n"))) + else if(giveRE) invisible(ae0) + } + } > if(FALSE) ## in future: ---------------------------------------- + source(system.file("xtraR/test-tools.R", package = "robustbase")) > ## > ## -> assert.EQ(), identical3(), .. > > > ## From /tests/reg-tests-1d.R (2022-08-09): > ## A good guess if we have _not_ translated error/warning/.. messages: > ## (should something like this be part of package tools ?) > englishMsgs <- { + ## 1. LANGUAGE takes precedence over locale settings: + if(nzchar(lang <- Sys.getenv("LANGUAGE"))) + lang == "en" + else { ## 2. Query the locale + if(!onWindows) { + ## sub() : + lc.msgs <- sub("\\..*", "", print(Sys.getlocale("LC_MESSAGES"))) + lc.msgs == "C" || substr(lc.msgs, 1,2) == "en" + } else { ## Windows + lc.type <- sub("\\..*", "", sub("_.*", "", print(Sys.getlocale("LC_CTYPE")))) + lc.type == "English" || lc.type == "C" + } + } + } > cat(sprintf("English messages: %s\n", englishMsgs)) English messages: FALSE > > > DNase1 <- DNase[ DNase$Run == 1, ] > Y <- DNase1[,"density"] # for convenience below > > ## classical > fm1 <- nls(density ~ Asym/(1 + exp(( xmid - log(conc) )/scal ) ), + data = DNase1, start = list(Asym = 3, xmid = 0, scal = 1), trace=TRUE) 14.32279 (3.02e+01): par = (3 0 1) 0.4542698 (9.73e+00): par = (2.115246 0.8410193 1.200064) 0.05869603 (3.34e+00): par = (2.446376 1.747516 1.189515) 0.005663523 (4.26e-01): par = (2.294087 1.412198 1.020463) 0.004791528 (2.02e-02): par = (2.341429 1.479688 1.040758) 0.004789569 (1.65e-04): par = (2.345135 1.483047 1.041439) 0.004789569 (1.98e-06): par = (2.345179 1.483089 1.041454) > summary(fm1) Formula: density ~ Asym/(1 + exp((xmid - log(conc))/scal)) Parameters: Estimate Std. Error t value Pr(>|t|) Asym 2.34518 0.07815 30.01 2.17e-13 *** xmid 1.48309 0.08135 18.23 1.22e-10 *** scal 1.04145 0.03227 32.27 8.51e-14 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.01919 on 13 degrees of freedom Number of iterations to convergence: 6 Achieved convergence tolerance: 1.985e-06 > wm1 <- update(fm1, weights = sqrt(conc)) # (weights as function of ) 27.10073 (3.68e+01): par = (3 0 1) 0.6008020 (8.66e+00): par = (2.182337 0.8948353 1.261465) 0.1716286 (4.40e+00): par = (2.51089 1.828486 1.208884) 0.01052871 (5.11e-01): par = (2.282185 1.401035 1.024226) 0.008359719 (6.68e-02): par = (2.359573 1.499564 1.050668) 0.008322484 (7.53e-04): par = (2.367424 1.506046 1.052066) 0.008322479 (1.52e-05): par = (2.367618 1.506233 1.052148) 0.008322479 (4.22e-07): par = (2.367622 1.506237 1.05215) > > ## robust > rm1 <- nlrob(formula(fm1), data = DNase1, trace = TRUE, + start = list(Asym = 3, xmid = 0, scal = 1)) robust iteration 1 14.32279 (3.02e+01): par = (3 0 1) 0.4542698 (9.73e+00): par = (2.115246 0.8410193 1.200064) 0.05869603 (3.34e+00): par = (2.446376 1.747516 1.189515) 0.005663523 (4.26e-01): par = (2.294087 1.412198 1.020463) 0.004791528 (2.02e-02): par = (2.341429 1.479688 1.040758) 0.004789569 (1.65e-04): par = (2.345135 1.483047 1.041439) 0.004789569 (1.98e-06): par = (2.345179 1.483089 1.041454) --> irls.delta(previous, resid) = 0.999803 -- *not* converged robust iteration 2 0.003971483 (6.54e-02): par = (2.345179 1.483089 1.041454) 0.003954569 (1.07e-03): par = (2.356445 1.495544 1.043788) 0.003954565 (2.77e-06): par = (2.356586 1.49565 1.043815) --> irls.delta(previous, resid) = 0.0614627 -- *not* converged robust iteration 3 0.003934724 (1.25e-02): par = (2.356586 1.49565 1.043815) 0.003934110 (8.81e-05): par = (2.358633 1.498205 1.044647) 0.003934110 (8.09e-07): par = (2.358657 1.498229 1.044655) --> irls.delta(previous, resid) = 0.0121515 -- *not* converged robust iteration 4 0.003930685 (4.06e-03): par = (2.358657 1.498229 1.044655) 0.003930620 (2.54e-05): par = (2.359307 1.499046 1.044928) 0.003930620 (2.52e-07): par = (2.359314 1.499053 1.044931) --> irls.delta(previous, resid) = 0.00395059 -- *not* converged robust iteration 5 0.003929580 (1.33e-03): par = (2.359314 1.499053 1.044931) 0.003929573 (8.06e-06): par = (2.359525 1.49932 1.04502) --> irls.delta(previous, resid) = 0.00128458 -- *not* converged robust iteration 6 0.003929244 (4.36e-04): par = (2.359525 1.49932 1.04502) 0.003929244 (2.63e-06): par = (2.359596 1.499409 1.04505) --> irls.delta(previous, resid) = 0.000423006 -- *not* converged robust iteration 7 0.003929132 (1.44e-04): par = (2.359596 1.499409 1.04505) 0.003929132 (8.01e-07): par = (2.35962 1.499438 1.04506) --> irls.delta(previous, resid) = 0.00013931 -- *not* converged robust iteration 8 0.003929095 (4.73e-05): par = (2.35962 1.499438 1.04506) 0.003929095 (3.05e-07): par = (2.359628 1.499448 1.045063) --> irls.delta(previous, resid) = 4.58377e-05 -- *not* converged robust iteration 9 0.003929083 (1.56e-05): par = (2.359628 1.499448 1.045063) 0.003929083 (1.67e-07): par = (2.35963 1.499451 1.045064) --> irls.delta(previous, resid) = 1.51092e-05 -- *not* converged robust iteration 10 0.003929079 (5.19e-06): par = (2.35963 1.499451 1.045064) > (sm1 <- summary(rm1)) Call: nlrob(formula = formula(fm1), data = DNase1, start = list(Asym = 3, xmid = 0, scal = 1), trace = TRUE, algorithm = "default") Residuals: Min 1Q Median 3Q Max -0.0322811 -0.0130976 -0.0008932 0.0095784 0.0404174 Parameters: Estimate Std. Error t value Pr(>|t|) Asym 2.35963 0.08627 27.35 7.10e-13 *** xmid 1.49945 0.09022 16.62 3.87e-10 *** scal 1.04506 0.03504 29.83 2.34e-13 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Robust residual standard error: 0.01829 Convergence in 10 IRWLS iterations Robustness weights: 14 weights are ~= 1. The remaining 2 ones are 11 13 0.6087 0.7621 > stopifnot(all.equal(Y, fitted(fm1) + residuals(fm1), check.attributes=FALSE), + ## fitted() has "label" attribute + identical3(c(fitted(fm1)), predict(fm1), predict(fm1, newdata=DNase1)), + ## robust fit : + identical3(fitted(rm1), predict(rm1), predict(rm1, newdata=DNase1)), + all.equal(Y, unname(fitted(rm1) + residuals(rm1)))) > print(coef(rm1), digits=12) Asym xmid scal 2.35963007990 1.49945087898 1.04506391536 > ## 2.35963008460 1.49945088410 1.04506391722 F19 Lx 64b > ## 2.35963008460 1.49945088410 1.04506391722 Win(Serv.2003) 64b > ## 2.35963008613 1.49945088600 1.04506391793 F19 Lx 32b > ## 2.35963008613 1.49945088600 1.04506391793 Win(Serv.2003) 32b > assert.EQ(coef(rm1), giveRE=TRUE, + c(Asym=2.35963008, xmid=1.49945088, scal=1.04506392), tol = 4e-8) Mean relative difference: 1.1747e-09 > assert.EQ(sqrt(diag(sm1$cov)), giveRE=TRUE, + ## 32b 0.08626872273, 0.0902194541, 0.03503833759 + c(Asym=0.0862687305, xmid=0.0902194608, scal=0.0350383389), + tol = 7e-7) Mean relative difference: 1.175526e-07 > ## examples with weights: > rm. <- update(rm1, weights = NULL)# 'NULL' but not missing() robust iteration 1 14.32279 (3.02e+01): par = (3 0 1) 0.4542698 (9.73e+00): par = (2.115246 0.8410193 1.200064) 0.05869603 (3.34e+00): par = (2.446376 1.747516 1.189515) 0.005663523 (4.26e-01): par = (2.294087 1.412198 1.020463) 0.004791528 (2.02e-02): par = (2.341429 1.479688 1.040758) 0.004789569 (1.65e-04): par = (2.345135 1.483047 1.041439) 0.004789569 (1.97e-06): par = (2.345179 1.483089 1.041454) --> irls.delta(previous, resid) = 0.999803 -- *not* converged robust iteration 2 0.003971483 (6.54e-02): par = (2.345179 1.483089 1.041454) 0.003954569 (1.07e-03): par = (2.356445 1.495544 1.043788) 0.003954565 (2.78e-06): par = (2.356586 1.49565 1.043815) --> irls.delta(previous, resid) = 0.0614627 -- *not* converged robust iteration 3 0.003934724 (1.25e-02): par = (2.356586 1.49565 1.043815) 0.003934110 (8.81e-05): par = (2.358633 1.498205 1.044647) 0.003934110 (7.02e-07): par = (2.358657 1.498229 1.044655) --> irls.delta(previous, resid) = 0.0121516 -- *not* converged robust iteration 4 0.003930685 (4.06e-03): par = (2.358657 1.498229 1.044655) 0.003930620 (2.54e-05): par = (2.359307 1.499046 1.044928) 0.003930620 (2.40e-07): par = (2.359314 1.499053 1.044931) --> irls.delta(previous, resid) = 0.00395059 -- *not* converged robust iteration 5 0.003929580 (1.33e-03): par = (2.359314 1.499053 1.044931) 0.003929573 (7.96e-06): par = (2.359525 1.49932 1.04502) --> irls.delta(previous, resid) = 0.00128457 -- *not* converged robust iteration 6 0.003929244 (4.36e-04): par = (2.359525 1.49932 1.04502) 0.003929244 (2.68e-06): par = (2.359596 1.499409 1.04505) --> irls.delta(previous, resid) = 0.000422935 -- *not* converged robust iteration 7 0.003929132 (1.44e-04): par = (2.359596 1.499409 1.04505) 0.003929132 (9.19e-07): par = (2.35962 1.499438 1.04506) --> irls.delta(previous, resid) = 0.000139325 -- *not* converged robust iteration 8 0.003929095 (4.74e-05): par = (2.35962 1.499438 1.04506) 0.003929095 (2.23e-07): par = (2.359628 1.499448 1.045063) --> irls.delta(previous, resid) = 4.59223e-05 -- *not* converged robust iteration 9 0.003929083 (1.56e-05): par = (2.359628 1.499448 1.045063) 0.003929083 (1.27e-07): par = (2.35963 1.499451 1.045064) --> irls.delta(previous, resid) = 1.50805e-05 -- *not* converged robust iteration 10 0.003929079 (5.15e-06): par = (2.35963 1.499451 1.045064) > ww <- sqrt(DNase1[,"conc"]) > wr1 <- update(rm1, weights = sqrt(conc), trace=FALSE) > wr1. <- update(rm1, weights = ww, trace=FALSE) > ii <- names(rm1) != "call" > stopifnot(all.equal(rm1[ii], rm.[ii], tol = 1e-15), + all.equal(wr1[ii],wr1.[ii], tol = 1e-15)) Error: rm1[ii] and rm.[ii] are not equal: Component "m": Component "resid": Component ".swts": Mean relative difference: 1.271931e-08 Component "m": Component "resid": Component "QR": Component "qr": Mean relative difference: 2.67232e-08 Component "m": Component "resid": Component "QR": Component "qraux": Mean relative difference: 3.689806e-09 .... Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [43s/46s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs See ‘/data/localhost/ripley/R/packages/tests-MKL/robustbase.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 3:37.81, 185.58 + 15.36