- using R Under development (unstable) (2025-12-18 r89199)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-15 (Debian 15.2.0-11) 15.2.0
GNU Fortran (Debian 15.2.0-11) 15.2.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
- checking for file ‘paths/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘paths’ version ‘0.1.1’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [1s/1s] OK
- 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 ‘paths’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... 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 ... [3s/3s] OK
- checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
- checking whether the package can be unloaded cleanly ... [3s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
- checking loading without being on the library search path ... [3s/3s] 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 ... [14s/16s] OK
- checking Rd files ... [0s/0s] 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 ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking examples ... [8s/10s] ERROR
Running examples in ‘paths-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.sens
> ### Title: Plot Method for 'sens' Objects
> ### Aliases: plot.sens
>
> ### ** Examples
>
> data(tatar)
>
> m1 <- c("trust_g1", "victim_g1", "fear_g1")
> m2 <- c("trust_g2", "victim_g2", "fear_g2")
> m3 <- c("trust_g3", "victim_g3", "fear_g3")
> mediators <- list(m1, m2, m3)
>
> formula_m0 <- annex ~ kulak + prosoviet_pre + religiosity_pre + land_pre +
+ orchard_pre + animals_pre + carriage_pre + otherprop_pre + violence
> formula_m1 <- update(formula_m0, ~ . + trust_g1 + victim_g1 + fear_g1)
> formula_m2 <- update(formula_m1, ~ . + trust_g2 + victim_g2 + fear_g2)
> formula_m3 <- update(formula_m2, ~ . + trust_g3 + victim_g3 + fear_g3)
> formula_ps <- violence ~ kulak + prosoviet_pre + religiosity_pre +
+ land_pre + orchard_pre + animals_pre + carriage_pre + otherprop_pre
>
> ####################################################
> # Causal Paths Analysis using GLM
> ####################################################
>
> # outcome models
> glm_m0 <- glm(formula_m0, family = binomial("logit"), data = tatar)
> glm_m1 <- glm(formula_m1, family = binomial("logit"), data = tatar)
> glm_m2 <- glm(formula_m2, family = binomial("logit"), data = tatar)
> glm_m3 <- glm(formula_m3, family = binomial("logit"), data = tatar)
> glm_ymodels <- list(glm_m0, glm_m1, glm_m2, glm_m3)
>
> # propensity score model
> glm_ps <- glm(formula_ps, family = binomial("logit"), data = tatar)
>
> # causal paths analysis using glm
> # note: For illustration purposes only a small number of bootstrap replicates are used
> paths_glm <- paths(a = "violence", y = "annex", m = mediators,
+ glm_ymodels, ps_model = glm_ps, data = tatar, nboot = 3)
....>
> # sensitivity analysis for the path-specific effect via M1
> sens_glm <- sens(paths_glm, confounded = "M1", estimand = "via M1",
+ gamma_values = - seq(0, 0.5, 0.005), eta_values = seq(-0.5, 0.5, 0.005))
>
> plot(sens_glm)
Error in `metR::geom_text_contour()`:
! Problem while converting geom to grob.
ℹ Error occurred in the 3rd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─base (local) `<fn>`(x)
2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
3. │ ├─ggplot2::ggplot_gtable(data)
4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
5. │ └─ggplot2:::by_layer(...)
6. │ ├─rlang::try_fetch(...)
7. │ │ ├─base::tryCatch(...)
8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. │ │ └─base::withCallingHandlers(...)
12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
13. │ └─l$draw_geom(d, layout)
14. │ └─ggplot2 (local) draw_geom(..., self = self)
15. │ └─self$geom$draw_layer(...)
16. │ └─ggplot2 (local) draw_layer(..., self = self)
17. │ └─base::lapply(...)
18. │ └─ggplot2 (local) FUN(X[[i]], ...)
19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
20. │ └─self$draw_panel(...)
21. │ └─metR (local) draw_panel(...)
22. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
23. │ └─data.table:::`[.data.table`(...)
24. └─base::.handleSimpleError(...)
25. └─rlang (local) h(simpleError(msg, call))
26. └─handlers[[1L]](cnd)
27. └─cli::cli_abort(...)
28. └─rlang::abort(...)
Execution halted
- checking PDF version of manual ... [4s/7s] OK
- checking HTML version of manual ... [1s/2s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR