* using log directory ‘/home/hornik/tmp/CRAN_special_donttest/delimtools.Rcheck’
* using R Under development (unstable) (2026-03-21 r89670)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-15 (Debian 15.2.0-14) 15.2.0
    GNU Fortran (Debian 15.2.0-14) 15.2.0
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-03-22 15:44:07 UTC
* using option ‘--run-donttest’
* checking for file ‘delimtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘delimtools’ version ‘0.2.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/6s] NOTE
Maintainer: ‘Pedro Bittencourt <pedro.sennabittencourt@gmail.com>’

New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2026-03-18 as issues were not corrected
    despite reminders.

Suggests or Enhances not in mainstream repositories:
  bGMYC, splits
Availability using Additional_repositories specification:
  bGMYC    yes   https://pedrosenna.github.io/drat/
  splits   yes   https://r-forge.r-project.org/    
* 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 ... [6s/6s] OK
* 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 ... [8s/8s] OK
* checking Rd files ... [0s/0s] 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 ... [1s/1s] 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 ... [4s/8s] ERROR
Running examples in ‘delimtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: confidence_intervals
> ### Title: Confidence Intervals for Species Delimitations Methods
> ### Aliases: confidence_intervals gmyc_ci bgmyc_ci locmin_ci mptp_ci
> 
> ### ** Examples
> 
> ## No test: 
> 
> # gmyc confidence intervals
> 
> # compute values using multisession mode
> try( {
+   future::plan("multisession")
+ 
+   gmyc_res <- gmyc_ci(ape::as.phylo(geophagus_beast), geophagus_posterior)
+ 
+   # reset future parameters
+   future::plan("sequential")
+ }
+ )
Error in loadNamespace(x) : there is no package called ‘splits’
> # plot distribution
> try(plot(density(gmyc_res)))
Error : object 'gmyc_res' not found
> 
> # tabulate
> try( tibble::tibble(
+   method = "gmyc",
+   point_estimate = gmyc_res[1],
+   CI_95 = as.integer(quantile(gmyc_res[-1], probs = c(0.025, 0.975))) |>
+     stringr::str_flatten(collapse = "-"),
+   CI_mean = as.integer(mean(gmyc_res[-1])),
+   CI_median = as.integer(stats::median(gmyc_res[-1]))
+ )
+ )
Error : object 'gmyc_res' not found
> ## End(No test)
> 
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("confidence_intervals", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
Error: connections left open:
	<-localhost:36396 (sockconn)
	<-localhost:36396 (sockconn)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE