• using R Under development (unstable) (2025-12-20 r89211)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.8     flang version 21.1.8
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘modelbased/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘modelbased’ version ‘0.13.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘modelbased’ can be installed ... [16s/45s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking whether startup messages can be suppressed ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [41s/104s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [31s/101s] ERROR Running examples in ‘modelbased-Ex.R’ failed The error most likely occurred in: > ### Name: estimate_slopes > ### Title: Estimate Marginal Effects > ### Aliases: estimate_slopes > > ### ** Examples > > ## Don't show: > if (all(insight::check_if_installed(c("marginaleffects", "emmeans", "effectsize", "mgcv", "ggplot2", "see"), quietly = TRUE))) withAutoprint({ # examplesIf + ## End(Don't show) + library(ggplot2) + # Get an idea of the data + ggplot(iris, aes(x = Petal.Length, y = Sepal.Width)) + + geom_point(aes(color = Species)) + + geom_smooth(color = "black", se = FALSE) + + geom_smooth(aes(color = Species), linetype = "dotted", se = FALSE) + + geom_smooth(aes(color = Species), method = "lm", se = FALSE) + + # Model it + model <- lm(Sepal.Width ~ Species * Petal.Length, data = iris) + # Compute the marginal effect of Petal.Length at each level of Species + slopes <- estimate_slopes(model, trend = "Petal.Length", by = "Species") + slopes + + # What is the *average* slope of Petal.Length? This can be calculated by + # taking the average of the slopes across all Species, using `comparison`. + # We pass a function to `comparison` that calculates the mean of the slopes. + estimate_slopes( + model, + trend = "Petal.Length", + by = "Species", + comparison = ~I(mean(x)) + ) + + ## Not run: + ##D # Plot it + ##D plot(slopes) + ##D standardize(slopes) + ##D + ##D model <- mgcv::gam(Sepal.Width ~ s(Petal.Length), data = iris) + ##D slopes <- estimate_slopes(model, by = "Petal.Length", length = 50) + ##D summary(slopes) + ##D plot(slopes) + ##D + ##D model <- mgcv::gam(Sepal.Width ~ s(Petal.Length, by = Species), data = iris) + ##D slopes <- estimate_slopes(model, + ##D trend = "Petal.Length", + ##D by = c("Petal.Length", "Species"), length = 20 + ##D ) + ##D summary(slopes) + ##D plot(slopes) + ##D + ##D # marginal effects, grouped by Species, at different values of Petal.Length + ##D estimate_slopes(model, + ##D trend = "Petal.Length", + ##D by = c("Petal.Length", "Species"), length = 10 + ##D ) + ##D + ##D # marginal effects at different values of Petal.Length + ##D estimate_slopes(model, trend = "Petal.Length", by = "Petal.Length", length = 10) + ##D + ##D # marginal effects at very specific values of Petal.Length + ##D estimate_slopes(model, trend = "Petal.Length", by = "Petal.Length=c(1, 3, 5)") + ##D + ##D # average marginal effects of Petal.Length, + ##D # just for the trend within a certain range + ##D estimate_slopes(model, trend = "Petal.Length=seq(2, 4, 0.01)") + ## End(Not run) + ## Don't show: + }) # examplesIf > library(ggplot2) > ggplot(iris, aes(x = Petal.Length, y = Sepal.Width)) + geom_point(aes(color = Species)) + + geom_smooth(color = "black", se = FALSE) + geom_smooth(aes(color = Species), + linetype = "dotted", se = FALSE) + geom_smooth(aes(color = Species), method = "lm", + se = FALSE) `geom_smooth()` using method = 'loess' and formula = 'y ~ x' `geom_smooth()` using method = 'loess' and formula = 'y ~ x' `geom_smooth()` using formula = 'y ~ x' > model <- lm(Sepal.Width ~ Species * Petal.Length, data = iris) > slopes <- estimate_slopes(model, trend = "Petal.Length", by = "Species") Error in `[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp) :   attempt access index 10/10 in VECTOR_ELT Calls: withAutoprint ... eval -> eval -> estimate_slopes -> get_marginaltrends Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [105s/183s] ERROR   Running ‘testthat.R’ [105s/181s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > # This file is part of the standard setup for testthat.   > # It is recommended that you do not modify it.   > #   > # Where should you do additional test configuration?   > #   > # * https://r-pkgs.org/tests.html   > # * https://testthat.r-lib.org/reference/test_package.html#special-files   > library(testthat)   > library(modelbased)   >   > test_check("modelbased")   Starting 2 test processes.   Saving _problems/test-attributes_estimatefun-108.R   Saving _problems/test-estimate_slopes-10.R   Saving _problems/test-estimate_slopes-63.R   Saving _problems/test-estimate_slopes-124.R   > test-multivariate_response.R: Confidence intervals are not yet supported for models of class `mlm`.   > test-multivariate_response.R: Confidence intervals are not yet supported for models of class `mlm`.   Saving _problems/test-transform_response-65.R   Saving _problems/test-visualisation_recipe-151.R   [ FAIL 6 | WARN 0 | SKIP 54 | PASS 194 ]      ══ Skipped tests (54) ══════════════════════════════════════════════════════════   • .Platform$OS.type == "windows" is not TRUE (1):     'test-estimate_predicted.R:58:3'   • On CRAN (45): 'test-backtransform_invlink.R:1:1', 'test-betareg.R:1:1',     'test-bias_correction.R:1:1', 'test-brms-marginaleffects.R:1:1',     'test-brms.R:1:1', 'test-equivalence.R:1:1',     'test-estimate_contrasts-average.R:1:1', 'test-estimate_contrasts.R:1:1',     'test-estimate_contrasts_bookexamples.R:1:1',     'test-estimate_contrasts_counterfactual.R:1:1',     'test-estimate_contrasts_effectsize.R:1:1',     'test-estimate_contrasts_inequality.R:1:1',     'test-estimate_contrasts_methods.R:1:1', 'test-estimate_filter.R:1:1',     'test-estimate_means-average.R:1:1', 'test-estimate_means.R:1:1',     'test-estimate_means_ci.R:1:1', 'test-estimate_means_counterfactuals.R:1:1',     'test-estimate_grouplevel.R:54:3', 'test-estimate_grouplevel.R:72:3',     'test-estimate_grouplevel.R:93:3', 'test-estimate_grouplevel.R:123:3',     'test-estimate_grouplevel.R:150:5', 'test-estimate_grouplevel.R:182:3',     'test-estimate_grouplevel.R:261:3', 'test-estimate_grouplevel.R:308:3',     'test-estimate_means_dotargs.R:1:1', 'test-estimate_means_mixed.R:1:1',     'test-estimate_means_marginalization.R:1:1', 'test-estimate_slopes.R:129:1',     'test-g_computation.R:1:1', 'test-get_marginaltrends.R:1:1',     'test-glmmTMB.R:1:1', 'test-joint_test.R:1:1', 'test-keep_iterations.R:1:1',     'test-maihda.R:1:1', 'test-mice.R:1:1', 'test-ordinal.R:1:1',     'test-plot-grouplevel.R:1:1', 'test-predict-dpar.R:1:1',     'test-standardize.R:1:1', 'test-summary_estimate_slopes.R:3:1',     'test-transform_response.R:3:1', 'test-vcov.R:1:1', 'test-zeroinfl.R:1:1'   • On Linux (8): 'test-plot-facet.R:1:1', 'test-plot-flexible_numeric.R:1:1',     'test-plot-ordinal.R:1:1', 'test-plot-slopes.R:1:1', 'test-plot.R:1:1',     'test-print.R:1:1', 'test-residualize_over_grid.R:1:1',     'test-scoping_issues.R:1:1'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-attributes_estimatefun.R:108:3'): attributes_means, slopes ─────   Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT   Backtrace:        ▆     1. ├─base::suppressMessages(...) at test-attributes_estimatefun.R:108:3     2. │ └─base::withCallingHandlers(...)     3. └─modelbased::estimate_slopes(model, "Sepal.Width", backend = "marginaleffects")     4. └─modelbased::get_marginaltrends(...)     5. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))     6. │ └─base::withCallingHandlers(...)     7. ├─base::do.call(marginaleffects::avg_slopes, fun_args)     8. ├─marginaleffects (local) `<fn>`(...)     9. │ └─base::eval.parent(call_attr)    10. │ └─base::eval(expr, p)    11. │ └─base::eval(expr, p)    12. ├─marginaleffects::slopes(...)    13. │ └─base::eval.parent(call_attr_c)    14. │ └─base::eval(expr, p)    15. │ └─base::eval(expr, p)    16. └─marginaleffects::comparisons(...)    17. ├─base::do.call("get_comparisons", args)    18. └─marginaleffects:::get_comparisons(...)    19. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]    20. └─data.table:::`[.data.table`(...)   ── Error ('test-estimate_slopes.R:10:3'): estimate_slopes ──────────────────────   Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT   Backtrace:        ▆     1. ├─base::suppressMessages(estimate_slopes(model, backend = "marginaleffects")) at test-estimate_slopes.R:10:3     2. │ └─base::withCallingHandlers(...)     3. └─modelbased::estimate_slopes(model, backend = "marginaleffects")     4. └─modelbased::get_marginaltrends(...)     5. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))     6. │ └─base::withCallingHandlers(...)     7. ├─base::do.call(marginaleffects::avg_slopes, fun_args)     8. ├─marginaleffects (local) `<fn>`(...)     9. │ └─base::eval.parent(call_attr)    10. │ └─base::eval(expr, p)    11. │ └─base::eval(expr, p)    12. ├─marginaleffects::slopes(...)    13. │ └─base::eval.parent(call_attr_c)    14. │ └─base::eval(expr, p)    15. │ └─base::eval(expr, p)    16. └─marginaleffects::comparisons(...)    17. ├─base::do.call("get_comparisons", args)    18. └─marginaleffects:::get_comparisons(...)    19. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]    20. └─data.table:::`[.data.table`(...)   ── Error ('test-estimate_slopes.R:63:3'): estimate_slopes, johnson-neyman p-adjust ──   Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT   Backtrace:        ▆     1. └─modelbased::estimate_slopes(model, "Petal.Width", by = "Petal.Length") at test-estimate_slopes.R:63:3     2. └─modelbased::get_marginaltrends(...)     3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))     4. │ └─base::withCallingHandlers(...)     5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)     6. ├─marginaleffects (local) `<fn>`(...)     7. │ └─base::eval.parent(call_attr)     8. │ └─base::eval(expr, p)     9. │ └─base::eval(expr, p)    10. ├─marginaleffects::slopes(...)    11. │ └─base::eval.parent(call_attr_c)    12. │ └─base::eval(expr, p)    13. │ └─base::eval(expr, p)    14. └─marginaleffects::comparisons(...)    15. ├─base::do.call("get_comparisons", args)    16. └─marginaleffects:::get_comparisons(...)    17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]    18. └─data.table:::`[.data.table`(...)   ── Error ('test-estimate_slopes.R:124:3'): estimate_slopes, custom comparison ──   Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT   Backtrace:        ▆     1. ├─modelbased::estimate_contrasts(...) at test-estimate_slopes.R:124:3     2. └─modelbased:::estimate_contrasts.default(...)     3. └─modelbased::get_marginalcontrasts(...)     4. └─modelbased::estimate_slopes(...)     5. └─modelbased::get_marginaltrends(...)     6. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))     7. │ └─base::withCallingHandlers(...)     8. ├─base::do.call(marginaleffects::avg_slopes, fun_args)     9. ├─marginaleffects (local) `<fn>`(...)    10. │ └─base::eval.parent(call_attr)    11. │ └─base::eval(expr, p)    12. │ └─base::eval(expr, p)    13. ├─marginaleffects::slopes(...)    14. │ └─base::eval.parent(call_attr_c)    15. │ └─base::eval(expr, p)    16. │ └─base::eval(expr, p)    17. └─marginaleffects::comparisons(...)    18. ├─base::do.call("get_comparisons", args)    19. └─marginaleffects:::get_comparisons(...)    20. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]    21. └─data.table:::`[.data.table`(...)   ── Error ('test-transform_response.R:65:3'): estimate_slopes, transform ────────   Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT   Backtrace:        ▆     1. └─modelbased::estimate_slopes(mod, trend = "Sepal.Width", by = "Species") at test-transform_response.R:65:3     2. └─modelbased::get_marginaltrends(...)     3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))     4. │ └─base::withCallingHandlers(...)     5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)     6. ├─marginaleffects (local) `<fn>`(...)     7. │ └─base::eval.parent(call_attr)     8. │ └─base::eval(expr, p)     9. │ └─base::eval(expr, p)    10. ├─marginaleffects::slopes(...)    11. │ └─base::eval.parent(call_attr_c)    12. │ └─base::eval(expr, p)    13. │ └─base::eval(expr, p)    14. └─marginaleffects::comparisons(...)    15. ├─base::do.call("get_comparisons", args)    16. └─marginaleffects:::get_comparisons(...)    17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]    18. └─data.table:::`[.data.table`(...)   ── Error ('test-visualisation_recipe.R:151:3'): visualization_recipe ───────────   Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 15/15 in VECTOR_ELT   Backtrace:        ▆     1. └─modelbased::estimate_slopes(model, trend = "Sepal.Width") at test-visualisation_recipe.R:151:3     2. └─modelbased::get_marginaltrends(...)     3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))     4. │ └─base::withCallingHandlers(...)     5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)     6. ├─marginaleffects (local) `<fn>`(...)     7. │ └─base::eval.parent(call_attr)     8. │ └─base::eval(expr, p)     9. │ └─base::eval(expr, p)    10. ├─marginaleffects::slopes(...)    11. │ └─base::eval.parent(call_attr_c)    12. │ └─base::eval(expr, p)    13. │ └─base::eval(expr, p)    14. └─marginaleffects::comparisons(...)    15. ├─base::do.call("get_comparisons", args)    16. └─marginaleffects:::get_comparisons(...)    17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]    18. └─data.table:::`[.data.table`(...)      [ FAIL 6 | WARN 0 | SKIP 54 | PASS 194 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... OK
• checking PDF version of manual ... [11s/25s] OK
• checking HTML version of manual ... [11s/34s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs