On 7/19/2026 8:22 PM, Kamil Bartoń wrote:
This worked for me: assignInNamespace("model.matrix.lme", \(object, ...) {data <- if (is.null(object$data)) eval(object$call$data) else object$data model.matrix(formula(object), data = data, contrasts.arg = object$contrasts)}, ns = "car")
Got it. Thanks a lot.
On 2026-07-19 13:59, Jinsong Zhao wrote:On 7/19/2026 7:39 PM, Kamil Bartoń wrote:I have tried to modify the car:::model.matrix.lme as suggested, however, it does not work.The problem may be that `car:::model.matrix.lme` uses: NextMethod(formula(object), [...]while the first argument for `NextMethod` should be a name of a generic function. This is why it is the lme object that is passed to `model.matrix.default` (which in turn looks for `model.frame.lme`, which is not implemented in "nlme") instead of a formula.I suppose the line in `car:::model.matrix.lme` should be changed to: model.frame(formula(object), [...]) to work as intended. ~kB> fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1) > car::Anova(fm2) Error in eval(extras, data, env) : object 'object' not found > traceback() 9: eval(extras, data, env) 8: eval(extras, data, env)7: model.frame.default(formula(object), data = data, contrasts.arg = object$contrasts) 6: model.frame(formula(object), data = data, contrasts.arg = object$contrasts)5: model.matrix.lme(mod) 4: model.matrix(mod) 3: Anova_II_lme(mod, vcov., singular.ok = singular.ok) 2: Anova.lme(fm2) 1: car::Anova(fm2)On 2026-07-19 13:21, varin sacha wrote:Sorry,There is no nlme:::model.frame.lme. That makes an S3 method signature mismatch the most likely explanation. The question of how best to resolve it is probably one for the MuMIn package maintainer.BestLe 19 juil. 2026 à 12:30, varin sacha via R-help <[email protected]> a écrit :Thanks Duncan. This seems like a promising workaround. You should try re-registering the multcomp method:registerS3method("model.frame", "lme", multcomp:::model.frame.lme) And then test: car::Anova(fm2)If this resolves the issue, it would provide strong evidence that the problem is caused by the incompatible MuMIn::model.frame.lme() S3 registration rather than by car::Anova() itself.Le 19 juil. 2026 à 12:14, Duncan Murdoch <[email protected]> a écrit :On 2026-07-19 4:55 a.m., Jinsong Zhao wrote:On 7/19/2026 3:52 PM, Jinsong Zhao wrote: On 7/19/2026 2:59 PM, Jinsong Zhao wrote:On 7/19/2026 2:38 PM, varin sacha wrote:Ok ! According to what I see, the error is occurring insidecar:::Anova.lme(), specifically during the construction of the modelmatrix.It therefore appears to be a genuine compatibility problem betweenthe current CRAN versions of car (3.1-5), piecewiseSEM (2.3.1), and/or nlme (3.1-170).The fact that you reproduced the same behavior on both Windows andFreeBSD also suggests that the issue is not platform-specific. I think this would be worth reporting to the package maintainers (perhaps starting with car, since the traceback shows that thefailure occurs inside Anova.lme(), while mentioning that the problem only arises after loading piecewiseSEM). The reproducible example you’ve provided should make it straightforward for them to investigate.The current maintainers of car and piecewiseSEM packages are alsocopied on this thread. As a regular user, I am just wondering what'sbehind the change in Anova()'s behavior—specifically, what gets modified after attaching piecewiseSEM? Best, JinsongA small step forward toward the root of the issue: I've justdiscovered that the model.frame.lme() function defined in the MuMIn package is what caused this problem (so I've copied this email to themaintainer of MuMIn).However, I'm still unclear as to why Anova() calls model.frame.lme()in the first place, given that car does not depend on the MuMInpackage. And directly invoking MuMIn:::model.frame.lme(fm2, random=TRUE) did not cause error.I think I've found the root cause.piecewiseSEM imports MuMIn, where model.frame.lme is registered as an S3method: S3method(model.frame, lme) Its definition is: model.frame.lme <- function(formula, random = FALSE, ...) But Anova() calls it (per traceback()) with: model.frame.lme(object, data, xlev = xlev)This passes data to the random argument, causing a type mismatch and theerror: Error in if (random) { : the condition has length > 1 I've diagnosed the issue, but I don't yet know how to fix it.This looks hard to fix.One problem is that there are two definitions for model.frame.lme, one from MuMIn and the other from multcomp. The one from MuMIn is being called. If the one in multcomp was called, things would be fine. Perhaps a fix could be for the MuMIn package to change its definition to something compatible with the multcomp definition, but the two functions appear to do different things. I don't know if they can be made compatible.Another problem is in the stats package. The stats:::model.matrix.default method makes a call todata <- model.frame(object, data, xlev = xlev) The definition of the generic model.frame() looks like function (formula, ...) UseMethod("model.frame")so stats:::model.matrix.default has no basis for assuming that the second argument is the data. Changing that call todata <- model.frame(object, data = data, xlev = xlev)would fix the issue of binding data to the "random" argument, but you'd still end up calling the "wrong" method.Maybe someone else has an elegant idea to fix this? Duncan MurdochBest, JinsongBest, Jinsonglibrary(MuMIn) library(nlme) library(car)Loading required package: carDatafm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1) Anova(fm2)Error in if (random) { : the condition has length > 1Le 19 juil. 2026 à 08:22, Jinsong Zhao <[email protected]> a écrit :Thank for the instruction. Here is the whole outputs:library(piecewiseSEM)Registered S3 method overwritten by 'lme4': method from na.action.merMod car This is piecewiseSEM version 2.3.0.2. Questions or bugs can be addressed to <[email protected]>.library(nlme) library(car)Loading required package: carDatafm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)Anova(fm2)Error in if (random) { : the condition has length > 1car::Anova(fm2)Error in if (random) { : the condition has length > 1car:::Anova.lme(fm2)Error in if (random) { : the condition has length > 1traceback()8: model.frame.lme(object, data, xlev = xlev) 7: model.frame(object, data, xlev = xlev)6: model.matrix.default(mod, data = structure(list(distance = c(26, 25, 29, 31, 21.5, 22.5, 23, 26.5, 23, 22.5, 24, 27.5, 25.5, 27.5, 26.5, 27, 20, 23.5, 22.5, 26, 24.5, 25.5, 27, 28.5, 22, 22, 24.5, 26.5, 24, 21.5, 24.5, 25.5, 23, 20.5, 31, 26, 27.5, 28, 31, 31.5, 23, 23, 23.5, 25, 21.5, 23.5, 24, 28, 17, 24.5, 26, 29.5, 22.5, 25.5, 25.5, 26, 23, 24.5, 26, 30, 22, 21.5, 23.5, 25, 21, 20, 21.5, 23, 21, 21.5, 24, 25.5, 20.5, 24, 24.5, 26, 23.5, 24.5, 25, 26.5, 21.5, 23, 22.5, 23.5, 20, 21, 21, 22.5, 21.5, 22.5, 23, 25, 23, 23, 23.5, 24, 20, 21, 22, 21.5, 16.5, 19, 19, 19.5, 24.5, 25, 28, 28), age = c(8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12,14, 8, 10, 12, 14, 8, 10, 12, 14, 8, 10, 12, 14), Subject = structure(c(15L,15L, 15L, 15L, 3L, 3L, 3L, 3L, 7L, 7L, 7L, 7L, 14L, 14L, 14L, 14L, 2L, 2L, 2L, 2L, 13L, 13L, 13L, 13L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 11L, 11L, 11L, 11L, 16L, 16L, 16L, 16L, 4L, 4L, 4L, 4L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 12L, 12L, 12L, 12L, 1L, 1L, 1L, 1L, 20L, 20L, 20L, 20L, 23L, 23L, 23L, 23L, 25L, 25L, 25L, 25L, 26L, 26L, 26L, 26L, 21L, 21L, 21L, 21L, 19L, 19L, 19L, 19L, 22L, 22L, 22L, 22L, 24L, 24L, 24L, 24L, 18L, 18L, 18L, 18L, 17L, 17L, 17L, 17L, 27L, 27L, 27L, 27L),levels = c("M16","M05", "M02", "M11", "M07", "M08", "M03", "M12", "M13", "M14", "M09", "M15", "M06", "M04", "M01", "M10", "F10", "F09", "F06", "F01", "F05", "F07", "F02", "F08", "F03", "F04", "F11"), class= c("ordered","factor")), Sex = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,2L, 2L, 2L, 2L), levels = c("Male", "Female"), class = "factor")), row.names = c("1","2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108"), outer= ~Sex, class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = distance ~age | Subject, labels = list(x = "Age", y = "Distance frompituitary to pterygomaxillary fissure"), units = list( x = "(yr)", y = "(mm)"), FUN = structure(function (x) max(x, na.rm = TRUE), source = "function (x) max(x, na.rm = TRUE)"), order.groups = TRUE),contrasts.arg = list(Sex = structure(c(0, 1), dim = 2:1,dimnames = list( c("Male", "Female"), "Female")))) 5: NextMethod(formula(object), data = data, contrasts.arg = object$contrasts) 4: model.matrix.lme(mod) 3: model.matrix(mod) 2: Anova_II_lme(mod, vcov., singular.ok = singular.ok) 1: car:::Anova.lme(fm2)sessionInfo()R version 4.6.1 (2026-06-24 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 10 x64 (build 19045) Matrix products: default LAPACK version 3.12.1 locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 [2] LC_CTYPE=Chinese (Simplified)_China.utf8 [3] LC_MONETARY=Chinese (Simplified)_China.utf8 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_China.utf8 time zone: Asia/Shanghai tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] car_3.1-5 carData_3.0-6 nlme_3.1-170 piecewiseSEM_2.3.1 loaded via a namespace (and not attached):[1] Matrix_1.7-5 jsonlite_2.0.0 compiler_4.6.1 Rcpp_1.1.2 [5] DiagrammeR_1.0.12 splines_4.6.1 boot_1.3-32 fastmap_1.2.0[9] lattice_0.22-9 TH.data_1.1-5 Formula_1.2-5 MuMIn_1.48.19 [13] rbibutils_2.4.1 htmlwidgets_1.6.4 MASS_7.3-66 visNetwork_2.1.4 [17] nloptr_2.2.1 insight_1.5.2 minqa_1.2.8 RColorBrewer_1.1-3 [21] rlang_1.3.0 multcomp_1.4-31 performance_0.17.1 estimability_2.0.0[25] cli_3.6.6 magrittr_2.0.5 Rdpack_2.6.6 emmeans_2.0.4[29] digest_0.6.39 grid_4.6.1 mvtnorm_1.4-2 sandwich_3.1-2[33] lme4_2.0-6 reformulas_0.4.4 glue_1.8.1 codetools_0.2-20[37] zoo_1.8-15 survival_3.8-9 abind_1.4-8 stats4_4.6.1 [41] tools_4.6.1 htmltools_0.5.9packageVersion("car")[1] ‘3.1.5’packageVersion("piecewiseSEM")[1] ‘2.3.1’packageVersion("nlme")[1] ‘3.1.170’All the packages are installed from CRAN, and updated to the latestversion. I also run the codes on FreeBSD 15.1, the same output. Best, JinsongOn 7/19/2026 2:02 PM, varin sacha wrote: Hi, Could this be a package compatibility bug?Since Anova(fm2), car::Anova(fm2), and even car:::Anova.lme(fm2)all produce the same error, it doesn’t appear to be a simple namespace masking issue. Could you post the output of: traceback() sessionInfo() packageVersion("car") packageVersion("piecewiseSEM") packageVersion("nlme") That should help identify the exact call that’s failing and whether the problem lies in car, piecewiseSEM, or an incompatibility between the two packages.Le 19 juil. 2026 à 04:58, Jinsong Zhao <[email protected]> a écrit :I have tried each solution in a new R session, and neither works.library(piecewiseSEM)Registered S3 method overwritten by 'lme4': method from na.action.merMod car This is piecewiseSEM version 2.3.0.2.Questions or bugs can be addressed to <[email protected]>.library(nlme) library(car)Loading required package: carDatafm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)Anova(fm2)Error in if (random) { : the condition has length > 1car::Anova(fm2)Error in if (random) { : the condition has length > 1car:::Anova.lme(fm2)Error in if (random) { : the condition has length > 1______________________________________________[email protected] mailing list -- To UNSUBSCRIBE and more, seehttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide https://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.______________________________________________ [email protected] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide https://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.______________________________________________ [email protected] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide https://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.______________________________________________ [email protected] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide https://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.______________________________________________ [email protected] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide https://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
______________________________________________ [email protected] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide https://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
