* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/JGL.Rcheck’
* using R Under development (unstable) (2025-06-17 r88325)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250425 (Red Hat 15.1.1-1)
    GNU Fortran (GCC) 15.1.1 20250425 (Red Hat 15.1.1-1)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘JGL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘JGL’ version ‘2.3.2’
* 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 ‘JGL’ can be installed ... [6s/23s] OK
* checking package 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 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 ... [12s/37s] 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 data for ASCII and uncompressed saves ... OK
* checking examples ... [7s/23s] ERROR
Running examples in ‘JGL-Ex.R’ failed
The error most likely occurred in:

> ### Name: net.edges
> ### Title: List the edges in a network
> ### Aliases: net.edges
> 
> ### ** Examples
> 
> ## load an example dataset with K=two classes, p=200 features, and n=100 samples per class:
> data(example.data)
> str(example.data)
List of 2
 $ : num [1:100, 1:200] 0.395 -2.03 -1.704 -0.469 1.75 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:200] "gene 1" "gene 2" "gene 3" "gene 4" ...
 $ : num [1:100, 1:200] -1.548 1.45 -0.812 -0.589 0.69 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:200] "gene 1" "gene 2" "gene 3" "gene 4" ...
> ## run fgl:
> fgl.results = JGL(Y=example.data,penalty="fused",lambda1=.25,lambda2=.1)
> ## get edges list:
> net.edges(fgl.results$theta)
[[1]]
Error in gsize(x) : 
  At vendor/cigraph/src/core/vector.pmt:516 : Assertion failed: v->stor_begin != NULL. This is an unexpected igraph error; please report this as a bug, along with the steps to reproduce it.
Please restart your R session to avoid crashes or other surprising behavior.
Calls: <Anonymous> ... stopifnot -> %+% -> stopifnot -> %+% -> stopifnot -> gsize
Execution halted
* checking PDF version of manual ... [7s/21s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-ATLAS/JGL.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:20.13, 52.87 + 7.44