* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ecoCopula.Rcheck’
* using R Under development (unstable) (2025-11-17 r89032)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.5 (1)
    Debian flang version 21.1.5 (1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘ecoCopula/DESCRIPTION’ ... OK
* this is package ‘ecoCopula’ version ‘1.0.4’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/124s] NOTE
Maintainer: ‘David Warton <david.warton@unsw.edu.au>’

New maintainer:
  David Warton <david.warton@unsw.edu.au>
Old maintainer(s):
  Gordana Popovic <g.popovic@unsw.edu.au>

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following (possibly) invalid URLs:
  URL: http://www.gnu.org/licenses/gpl-2.0.html
    From: README.md
    Status: Error
    Message: Timeout was reached [www.gnu.org]:
      Connection timed out after 60002 milliseconds
* 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 ‘ecoCopula’ can be installed ... [5s/5s] 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 ... 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 ... [0s/0s] 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 ... [2s/2s] ERROR
Running examples in ‘ecoCopula-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cgr
> ### Title: Fitting Gaussian copula graphical lasso to co-occurrence data
> ### Aliases: cgr
> 
> ### ** Examples
> 
> abund <- spider$abund[,1:5]
> spider_mod <- stackedsdm(abund,~1, data = spider$x, ncores=2) 
> spid_graph=cgr(spider_mod)

fatal Fortran runtime error(/tmp/Rtmpl1VjZT/R.INSTALL3860f546095410/glasso/src/glasso.f:376): Internal error: RUNTIME_CHECK(xCatKind->first == XCAT) failed at flang/runtime/matmul.cpp(457)
Aborted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [4s/4s] ERROR
  Running ‘testthat.R’ [4s/4s]
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(ecoCopula)
  Loading required package: mvabund
  > 
  > test_check("ecoCopula")
  
  fatal Fortran runtime error(/tmp/Rtmpl1VjZT/R.INSTALL3860f546095410/glasso/src/glasso.f:376): Internal error: RUNTIME_CHECK(xCatKind->first == XCAT) failed at flang/runtime/matmul.cpp(457)
  Aborted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [3s/3s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ecoCopula.Rmd’ using rmarkdown

fatal Fortran runtime error(/tmp/Rtmpl1VjZT/R.INSTALL3860f546095410/glasso/src/glasso.f:376): Internal error: RUNTIME_CHECK(xCatKind->first == XCAT) failed at flang/runtime/matmul.cpp(457)
Aborted

* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 ERRORs, 1 NOTE