- using R Under development (unstable) (2026-02-06 r89378)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-15 (Debian 15.2.0-12) 15.2.0
GNU Fortran (Debian 15.2.0-12) 15.2.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-02-07 14:05:49 UTC
- checking for file ‘bioLeak/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘bioLeak’ version ‘0.1.0’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [1s/2s] 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 ‘bioLeak’ 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 ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] 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 ... [16s/19s] 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [5s/7s] ERROR
Running examples in ‘bioLeak-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: audit_report
> ### Title: Render an HTML audit report
> ### Aliases: audit_report
>
> ### ** Examples
>
> set.seed(1)
> df <- data.frame(
+ subject = rep(1:6, each = 2),
+ outcome = factor(rep(c(0, 1), 6)),
+ x1 = rnorm(12),
+ x2 = rnorm(12)
+ )
>
> splits <- make_split_plan(df, outcome = "outcome",
+ mode = "subject_grouped", group = "subject",
+ v = 3, progress = FALSE)
>
> custom <- list(
+ glm = list(
+ fit = function(x, y, task, weights, ...) {
+ stats::glm(y ~ ., data = data.frame(y = y, x),
+ family = stats::binomial(), weights = weights)
+ },
+ predict = function(object, newdata, task, ...) {
+ as.numeric(stats::predict(object,
+ newdata = as.data.frame(newdata),
+ type = "response"))
+ }
+ )
+ )
>
> fit <- fit_resample(df, outcome = "outcome", splits = splits,
+ learner = "glm", custom_learners = custom,
+ metrics = "auc", refit = FALSE, seed = 1)
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>
> audit <- audit_leakage(fit, metric = "auc", B = 5, perm_stratify = FALSE)
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>
> if (requireNamespace("rmarkdown", quietly = TRUE) &&
+ requireNamespace("ggplot2", quietly = TRUE)) {
+ out_file <- audit_report(audit, output_dir = tempdir(), quiet = TRUE)
+ out_file
+ }
Warning in file(con, "w") :
cannot open file 'audit_report.knit.md': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: audit_report ... <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [16s/21s] OK
Running ‘testthat.R’ [16s/20s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [53s/71s] OK
- checking PDF version of manual ... [5s/7s] OK
- checking HTML version of manual ... [2s/4s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR