- using R version 4.5.1 (2025-06-13)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (Debian 14.3.0-5) 14.3.0
GNU Fortran (Debian 14.3.0-5) 14.3.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
- checking for file ‘graphPAF/DESCRIPTION’ ... OK
- this is package ‘graphPAF’ version ‘2.0.0’
- 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 ‘graphPAF’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... 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 ... [2s/3s] 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/3s] OK
- checking loading without being on the library search path ... [2s/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 ... [21s/27s] OK
- checking Rd files ... [0s/1s] 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 sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [16s/20s] ERROR
Running examples in ‘graphPAF-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.SAF_summary
> ### Title: Produce plots of sequential and average PAF
> ### Aliases: plot.SAF_summary
>
> ### ** Examples
>
> library(splines)
> library(survival)
> library(parallel)
> options(boot.parallel="snow")
> options(boot.ncpus=2)
> # Simulated data on occupational and environmental exposure to
> # chronic cough from Eide, 1995
> # First specify the causal graph, in terms of the parents of each node. Then put into a list
> parent_urban.rural <- c()
> parent_smoking.category <- c("urban.rural")
> parent_occupational.exposure <- c("urban.rural")
> parent_y <- c("urban.rural","smoking.category","occupational.exposure")
> parent_list <- list(parent_urban.rural, parent_smoking.category,
+ parent_occupational.exposure, parent_y)
> # also specify nodes of graph, in order from root to leaves
> node_vec <- c("urban.rural","smoking.category","occupational.exposure", "y")
> model_list=automatic_fit(Hordaland_data,
+ parent_list=parent_list, node_vec=node_vec, prev=.09)
Warning in eval(family$initialize) :
non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
non-integer #successes in a binomial glm!
> out <- average_paf(data=model_list[[length(model_list)]]$data,
+ model_list=model_list,
+ parent_list=parent_list, node_vec=node_vec, prev=.09, nperm=10,
+ riskfactor_vec = c("urban.rural","occupational.exposure"),ci=FALSE)
> plot(out)
Warning in fortify(data, ...) : Arguments in `...` must be used.
✖ Problematic argument:
• size = point.size
ℹ Did you misspell an argument name?
Error: Can't find method for generic `+(e1, e2)`:
- e1: <ggplot2::element_text>
- e2: <theme>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot.PAF_q 4.273 0.132 5.387
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [1s/1s] OK
- checking PDF version of manual ... [9s/12s] OK
- checking HTML version of manual ... [1s/2s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR