* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/delimtools.Rcheck’
* using R Under development (unstable) (2025-12-15 r89172)
* 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 ‘delimtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘delimtools’ version ‘0.2.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking: 'bGMYC', 'splits'
* 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 ‘delimtools’ can be installed ... OK
* 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 ... 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 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 ... [11s/11s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... INFO
Packages unavailable to check Rd xrefs: ‘bGMYC’, ‘splits’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/20s] OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘delimtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: abgd_tbl
> ### Title: A Command-Line Interface for ABGD - Automatic Barcode Gap
> ###   Discovery
> ### Aliases: abgd_tbl
> 
> ### ** Examples
> 
> ## No test: 
> 
> #' # get path to fasta file
> path_to_file <- system.file("extdata/geophagus.fasta", package = "delimtools")
> 
> # run ABGD
> abgd_df <- abgd_tbl(
+   infile = path_to_file,
+   exe = "/usr/local/bin/abgd",
+   model = 3,
+   slope = 0.5,
+   outfolder = NULL
+ )
Error in `abgd_tbl()`:
! Error: Please provide a valid path to the ABGD executable file.
Backtrace:
    ▆
 1. └─delimtools::abgd_tbl(...)
 2.   └─cli::cli_abort("Error: Please provide a valid path to the ABGD executable file.")
 3.     └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... 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
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/delimtools.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:50.40, 86.80 + 17.98