Re: [R] Anova() in car not works after loading piecewiseSEM package

[Jinsong Zhao]

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 inside 
car:::Anova.lme(), specifically during the construction of the model 
matrix.

It therefore appears to be a genuine compatibility problem between 
the 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 and 
FreeBSD 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 the 
failure 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 also 
copied on this thread. As a regular user, I am just wondering what's 
behind the change in Anova()'s behavior—specifically, what gets 
modified after attaching piecewiseSEM?

Best,

Jinsong

A small step forward toward the root of the issue: I've just 
discovered that the model.frame.lme() function defined in the MuMIn 
package is what caused this problem (so I've copied this email to the 
maintainer 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 MuMIn 
package. 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 S3 
method:

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 the 
error:

Error in if (random) { : the condition has length > 1

I've diagnosed the issue, but I don't yet know how to fix it.

Best,
Jinsong


Best,

Jinsong

> library(MuMIn)
> library(nlme)
> library(car)
Loading required package: carData
> fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
> Anova(fm2)
Error in if (random) { : the condition has length > 1



Le 19 juil. 2026 à 08:22, Jinsong Zhao <jsz...@yeah.net> 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 <jslef...@gmail.com>.
library(nlme)
library(car)
Loading required package: carData
fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
Anova(fm2)
Error in if (random) { : the condition has length > 1
car::Anova(fm2)
Error in if (random) { : the condition has length > 1
car:::Anova.lme(fm2)
Error in if (random) { : the condition has length > 1
traceback()
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 from 
pituitary 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_0.5.9
packageVersion("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 latest 
version. I also run the codes on FreeBSD 15.1, the same output.

Best,

Jinsong

On 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 <jsz...@yeah.net> 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 <jslef...@gmail.com>.
library(nlme)
library(car)
Loading required package: carData
fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
Anova(fm2)
Error in if (random) { : the condition has length > 1
car::Anova(fm2)
Error in if (random) { : the condition has length > 1
car:::Anova.lme(fm2)
Error in if (random) { : the condition has length > 1

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______________________________________________
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PLEASE do read the posting guide 
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and provide commented, minimal, self-contained, reproducible code.

______________________________________________
R-help@r-project.org 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.