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

Sorry,

There is no nlme:::model.frame.lme. That makes an S3 method signature misma=
tch the most likely explanation. The question of how best to resolve it is =
probably one for the MuMIn package maintainer.

Best


> Le 19 juil. 2026 =C3=A0 12:30, varin sacha via R-help <[email protected]=
rg> a =C3=A9crit :
> =

> =EF=BB=BFThanks Duncan. This seems like a promising workaround. You shoul=
d 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 pro=
blem is caused by the incompatible MuMIn::model.frame.lme() S3 registration=
 rather than by car::Anova() itself.
> =

> =

> =

> =

>> Le 19 juil. 2026 =C3=A0 12:14, Duncan Murdoch <[email protected]>=
 a =C3=A9crit :
>> =

>> =EF=BB=BFOn 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=E2=80=99ve provided should make it straightforward for them to i=
nvestigate.
>>>>> =

>>>>> 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=E2=80=94specifically, what ge=
ts
>>>>> 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=3D
>>>> 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 =3D FALSE, ...)
>>> But Anova() calls it (per traceback()) with:
>>> model.frame.lme(object, data, xlev =3D 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, one f=
rom 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 co=
uld be for the MuMIn package to change its definition to something compatib=
le with the multcomp definition, but the two functions appear to do differe=
nt things.  I don't know if they can be made compatible.
>> =

>> Another problem is in the stats package.  The stats:::model.matrix.defau=
lt method makes a call to
>> =

>> data <- model.frame(object, data, xlev =3D 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 secon=
d argument is the data.  Changing that call to
>> =

>> data <- model.frame(object, data =3D data, xlev =3D 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 Murdoch
>> =

>>> Best,
>>> Jinsong
>>>> Best,
>>>> =

>>>> Jinsong
>>>> =

>>>>> library(MuMIn)
>>>>> library(nlme)
>>>>> library(car)
>>>> Loading required package: carData
>>>>> fm2 <- lme(distance ~ age + Sex, data =3D Orthodont, random =3D ~ 1)
>>>>> Anova(fm2)
>>>> Error in if (random) { : the condition has length > 1
>>>> =

>>>> =

>>>>>> =

>>>>>>> Le 19 juil. 2026 =C3=A0 08:22, Jinsong Zhao <[email protected]> a =C3=
=A9crit :
>>>>>>> =

>>>>>>> =EF=BB=BFThank 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 =3D Orthodont, random =3D ~ =
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 =3D xlev)
>>>>>>> 7: model.frame(object, data, xlev =3D xlev)
>>>>>>> 6: model.matrix.default(mod, data =3D structure(list(distance =3D 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 =3D 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 =3D
>>>>>>> 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 =3D 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
>>>>>>> =3D c("ordered",
>>>>>>>    "factor")), Sex =3D 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 =3D c("Male", "Female"), class =3D
>>>>>>> "factor")), row.names =3D 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
>>>>>>> =3D ~Sex, class =3D c("nfnGroupedData",
>>>>>>>    "nfGroupedData", "groupedData", "data.frame"), formula =3D
>>>>>>> distance ~
>>>>>>>        age | Subject, labels =3D list(x =3D "Age", y =3D "Distance =
from
>>>>>>> pituitary to pterygomaxillary fissure"), units =3D list(
>>>>>>>        x =3D "(yr)", y =3D "(mm)"), FUN =3D structure(function (x)
>>>>>>>    max(x, na.rm =3D TRUE), source =3D "function (x) max(x, na.rm =
=3D
>>>>>>> TRUE)"), order.groups =3D TRUE),
>>>>>>>        contrasts.arg =3D list(Sex =3D structure(c(0, 1), dim =3D 2:=
1,
>>>>>>> dimnames =3D list(
>>>>>>>            c("Male", "Female"), "Female"))))
>>>>>>> 5: NextMethod(formula(object), data =3D data, contrasts.arg =3D
>>>>>>> object$contrasts)
>>>>>>> 4: model.matrix.lme(mod)
>>>>>>> 3: model.matrix(mod)
>>>>>>> 2: Anova_II_lme(mod, vcov., singular.ok =3D 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=3DChinese (Simplified)_China.utf8
>>>>>>> [2] LC_CTYPE=3DChinese (Simplified)_China.utf8
>>>>>>> [3] LC_MONETARY=3DChinese (Simplified)_China.utf8
>>>>>>> [4] LC_NUMERIC=3DC
>>>>>>> [5] LC_TIME=3DChinese (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] =E2=80=983.1.5=E2=80=99
>>>>>>>> packageVersion("piecewiseSEM")
>>>>>>> [1] =E2=80=982.3.1=E2=80=99
>>>>>>>> packageVersion("nlme")
>>>>>>> [1] =E2=80=983.1.170=E2=80=99
>>>>>>> =

>>>>>>> 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=E2=80=99t appear to be a simp=
le
>>>>>>>> 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=E2=80=99s failing and
>>>>>>>> whether the problem lies in car, piecewiseSEM, or an
>>>>>>>> incompatibility between the two packages.
>>>>>>>> =

>>>>>>>> =

>>>>>>>> =

>>>>>>>>>>> Le 19 juil. 2026 =C3=A0 04:58, Jinsong Zhao <[email protected]> a=
 =C3=A9crit :
>>>>>>>>>> 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 =3D Orthodont, random =3D=
 ~ 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
>>>>>> =

>>>>>> ______________________________________________
>>>>>> [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
>>>>> 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
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide https://www.R-project.org/posting-guid=
e.html
>>> 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.