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

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.

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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