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

Duncan Murdoch Sun, 19 Jul 2026 03:20:48 -0700

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 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.


This looks hard to fix.

One problem is that there are two definitions for model.frame.lme, onefrom MuMIn and the other from multcomp. The one from MuMIn is beingcalled. If the one in multcomp was called, things would be fine.Perhaps a fix could be for the MuMIn package to change its definition tosomething compatible with the multcomp definition, but the two functionsappear to do different things. I don't know if they can be made compatible.

Another problem is in the stats package. Thestats:::model.matrix.default method makes a call to


  data <- 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 thesecond argument is the data. Changing that call to


  data <- model.frame(object, data = data, xlev = xlev)

would fix the issue of binding data to the "random" argument, but you'dstill end up calling the "wrong" method.


Maybe someone else has an elegant idea to fix this?

Duncan Murdoch


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 <[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: 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 <[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: 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.


______________________________________________
[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.


______________________________________________
[email protected] mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide https://www.R-project.org/posting-guide.html
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Re: [R] Anova() in car not works after loading piecewiseSEM package

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