* using log directory ‘/data/localhost/ripley/R/packages/tests-BLIS/netgwas.Rcheck’
* using R Under development (unstable) (2026-11-12 r90880)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.2.1 20261029 (Red Hat 16.2.1-3)
    GNU Fortran (GCC) 16.2.1 20261029 (Red Hat 16.2.1-3)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-11-13 13:13:13 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘netgwas/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netgwas’ version ‘1.14.5’
* 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 ‘netgwas’ can be installed ... 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 ... [13s/28s] NOTE
Found calls to structure() using deprecated special names:
  netgwas/tests/testthat/test_cutoffs.R (.Dim: 2)
  netgwas/tests/testthat/test_lower.upper.R (.Dim: 3, .Names: 1)
'.Dim' should be changed to 'dim'.
'.Names' should be changed to 'names'.
* 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 ... [18s/39s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [19s/39s]
 [19s/39s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(netgwas)
  Registered S3 method overwritten by 'netgwas':
    method      from
    plot.select huge
  > 
  > test_check("netgwas")
  Constructing linkage map is in progress ... 
   
  Constructing linkage map is done.             
  Constructing linkage map is in progress ... 
   
  Constructing linkage map is done.             
  Constructing linkage map is in progress:100% 
  Constructing linkage map is done.             
  Constructing linkage map is in progress:100% 
  Constructing linkage map is done.             
  Reconstructing genotype-phenotypes networks is in progress ... 
   
  Reconstructing genotype-phenotype networks done. 
   
  Reconstructing genotype-phenotypes networks is in progress ... :100% 
  Reconstructing genotype-phenotypes networks done.  
  Reconstructing intra- and inter- chromosomal interactions network is in progress ... 
   
  Reconstructing intra- and inter- chromosomal interactions network done. 
   
  Reconstructing intra- and inter- chromosomal interactions network is in progress:100% 
  Reconstructing intra- and inter- chromosomal interactions network done.    
  Reconstructing intra- and inter- chromosomal interactions network is in progress:100% 
  Reconstructing intra- and inter- chromosomal interactions network done.    
  Reconstructing intra- and inter- chromosomal interactions network is in progress ... 
   
  Reconstructing intra- and inter- chromosomal interactions network done. 
   
  Calculating extended Bayesian information criterion (ebic) selection ...done.
  Saving _problems/test_selectnet-9.R
  [ FAIL 1 | WARN 128 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_selectnet.R:9:13'): Model selection works fine  ──────────────
  Expected `sel.ebic` to equal 4.
  Differences:
  1/1 mismatches
  [1] 3 - 4 == -1
  
  [ FAIL 1 | WARN 128 | SKIP 0 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... [5s/10s] 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, 1 NOTE
See
  ‘/data/localhost/ripley/R/packages/tests-BLIS/netgwas.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:04.65, 92.79 + 7.42