- using R Under development (unstable) (2025-09-16 r88840)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- 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
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- 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 ... [20s/112s] OK
See the install log for details.
- 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 ... [3s/22s] OK
- checking whether the package can be loaded with stated dependencies ... [3s/19s] OK
- checking whether the package can be unloaded cleanly ... [3s/10s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s/19s] OK
- checking whether the namespace can be unloaded cleanly ... [4s/19s] OK
- checking loading without being on the library search path ... [4s/24s] 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 ... [35s/216s] 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 sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [26s/123s] ERROR
Running examples in ‘graphPAF-Ex.R’ failed
The error most likely occurred in:
> ### 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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
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- checking PDF version of manual ... [11s/67s] OK
- checking HTML version of manual ... [2s/23s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR