* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GencoDymo2.Rcheck’
* using R Under development (unstable) (2025-07-13 r88407)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux 13 (trixie)
* using session charset: UTF-8
* checking for file ‘GencoDymo2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GencoDymo2’ version ‘1.0.1’
* 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 serialization versions ... OK
* checking whether package ‘GencoDymo2’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/GencoDymo2-00install.html' 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 ... [16s/20s] OK
* checking whether the package can be loaded with stated dependencies ... [16s/21s] OK
* checking whether the package can be unloaded cleanly ... [15s/21s] OK
* checking whether the namespace can be loaded with stated dependencies ... [16s/22s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/21s] OK
* checking loading without being on the library search path ... [16s/21s] OK
* checking whether startup messages can be suppressed ... [16s/20s] 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 ... [66s/82s] 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 ... [19s/25s] ERROR
Running examples in ‘GencoDymo2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_latest_release
> ### Title: Get the Latest Gencode Release Dynamically
> ### Aliases: get_latest_release
> 
> ### ** Examples
> 
> # Retrieve the latest release version for human
> human_release <- get_latest_release(species = "human", verbose = FALSE)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to ftp.ebi.ac.uk port 443 after 116 ms: Could not connect to server
Calls: get_latest_release -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [16s/20s] ERROR
  Running ‘testthat.R’ [16s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(GencoDymo2)
  Welcome to GencoDymo2 (v1.0.1)!
  Tools for dynamic GENCODE annotation analysis.
  > 
  > test_check("GencoDymo2")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-files.R:3:3'): get_latest_release works for human species ──────
  <COULDNT_CONNECT/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(7L, "Failed to connect to ftp.ebi.ac.uk port 443 after 33 ms: Could not connect to server", 
      TRUE)`: Failed to connect to ftp.ebi.ac.uk port 443 after 33 ms: Could not connect to server
  Backtrace:
      ▆
   1. ├─GencoDymo2::get_latest_release("human", verbose = FALSE) at test-files.R:3:3
   2. │ └─RCurl::getURL(url, ftp.use.epsv = FALSE, dirlistonly = TRUE)
   3. │   └─RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   4. └─RCurl (local) `<fn>`(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [4s/5s] OK
* checking PDF version of manual ... [5s/6s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 2 ERRORs