* using log directory ‘/srv/hornik/tmp/CRAN_pretest/paths.Rcheck’
* using R Under development (unstable) (2025-12-21 r89216)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.6 (2)
    Debian flang version 21.1.6 (2)
* 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 ‘0.1.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/4s] NOTE
Maintainer: ‘Xiang Zhou <xiang_zhou@fas.harvard.edu>’

New maintainer:
  Xiang Zhou <xiang_zhou@fas.harvard.edu>
Old maintainer(s):
  Minh Trinh <mdtrinh@mit.edu>
* 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 ... [6s/6s] OK
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [9s/9s] 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 ... [4s/4s] 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 ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE