- using R version 4.6.0 beta (2026-04-12 r89879)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-15 (Debian 15.2.0-16) 15.2.0
GNU Fortran (Debian 15.2.0-16) 15.2.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-04-15 10:35:54 UTC
- checking for file ‘diagFDR/DESCRIPTION’ ... OK
- this is package ‘diagFDR’ version ‘0.1.0’
- 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 ‘diagFDR’ 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 ... [1s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
- checking loading without being on the library search path ... [1s/1s] 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 ... [12s/16s] OK
- checking Rd files ... [1s/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 ... [20s/26s] ERROR
Running examples in ‘diagFDR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dfdr_render_report
> ### Title: Render a human-readable HTML report from 'dfdr_run_all' output
> ### Aliases: dfdr_render_report
>
> ### ** Examples
>
> # A minimal example that renders a report from a toy dataset.
> # This example is conditional because rmarkdown is in Suggests.
> if (requireNamespace("rmarkdown", quietly = TRUE)) {
+ library(tibble)
+ tmpdir <- tempdir()
+
+ set.seed(1)
+ n <- 3000
+ df <- tibble(
+ id = as.character(seq_len(n)),
+ run = "run1",
+ is_decoy = sample(c(FALSE, TRUE), n, replace = TRUE, prob = c(0.95, 0.05)),
+ score = rnorm(n),
+ q = pmin(1, rank(-score) / n),
+ pep = NA_real_
+ )
+ x <- as_dfdr_tbl(df, unit = "psm", scope = "global", q_source = "toy")
+
+ diag <- dfdr_run_all(
+ xs = list(toy = x),
+ alpha_main = 0.01,
+ compute_pseudo_pvalues = FALSE
+ )
+
+ # Render to a temporary directory (does not open a browser during checks)
+ dfdr_render_report(diag, out_dir = tmpdir, open = FALSE)
+ }
Warning in file(con, "w") :
cannot open file 'dfdr_report.knit.md': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: dfdr_render_report ... <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [83s/106s] OK
- checking PDF version of manual ... [9s/11s] OK
- checking HTML version of manual ... [7s/12s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR