* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/sigminer.Rcheck’
* using R Under development (unstable) (2025-12-24 r89227)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘sigminer/DESCRIPTION’ ... OK
* this is package ‘sigminer’ version ‘2.3.1’
* 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 ‘sigminer’ can be installed ... [58s/62s] OK
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘show_group_enrichment.R’
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [69s/72s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [39s/40s] OK
* checking examples with --run-donttest ... [11m/12m] ERROR
Running examples in ‘sigminer-Ex.R’ failed
The error most likely occurred in:

> ### Name: show_cn_profile
> ### Title: Show Sample Copy Number Profile
> ### Aliases: show_cn_profile
> 
> ### ** Examples
> 
> # Load copy number object
> load(system.file("extdata", "toy_copynumber.RData",
+   package = "sigminer", mustWork = TRUE
+ ))
> 
> p <- show_cn_profile(cn, nrow = 2, ncol = 1)
> p
> ## No test: 
> p2 <- show_cn_profile(cn,
+   nrow = 2, ncol = 1,
+   position = "chr1:3218923-116319008"
+ )
Error in data.table::foverlaps(data, position_df) : 
  attempt access index -1/2 in VECTOR_ELT
Calls: show_cn_profile -> <Anonymous>
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [53s/53s] OK
* checking PDF version of manual ... [12s/13s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/sigminer.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 18:23.10, 1018.23 + 52.10