* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/multiDEGGs.Rcheck’
* using R Under development (unstable) (2026-03-30 r89743)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-03-31 02:53:00 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘multiDEGGs/DESCRIPTION’ ... OK
* this is package ‘multiDEGGs’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘nestedcv’
* 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 ‘multiDEGGs’ can be installed ... [7s/12s] OK
* checking package directory ... 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 ... 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 ... [11s/15s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘nestedcv’ in Rd xrefs
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘multiDEGGs-Ex.R’ failed
The error most likely occurred in:

> ### Name: multiDEGGs_combined_filter
> ### Title: Combined multiDEGGs filter
> ### Aliases: multiDEGGs_combined_filter
> 
> ### ** Examples
> 
> library(nestedcv)
Error in library(nestedcv) : there is no package called ‘nestedcv’
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
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(multiDEGGs)
  > 
  > test_check("multiDEGGs")
  there is no package called 'qvalue'
  Saving _problems/test-core_functions-81.R
  Saving _problems/test-core_functions-82.R
  Saving _problems/test-core_functions-85.R
  Saving _problems/test-core_functions-86.R
  Saving _problems/test-core_functions-88.R
  Saving _problems/test-core_functions-89.R
  there is no package called 'qvalue'
  there is no package called 'qvalue'
  [ FAIL 7 | WARN 0 | SKIP 3 | PASS 29 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-plotting_functions.R:39:3'
  • {nestedcv} is not installed (2): 'test-ML_functions.R:3:3',
    'test-ML_functions.R:52:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-core_functions.R:80:1'): test get_multiOmics_diffNetworks multi_omics ──
  Expected `colnames(res$Responder)` to equal `c("from", "to", "p.value", "p.adj", "layer")`.
  Differences:
  `actual`:   "layer"                               
  `expected`: "from"  "to" "p.value" "p.adj" "layer"
  
  ── Failure ('test-core_functions.R:82:1'): test get_multiOmics_diffNetworks multi_omics ──
  Expected `nrow(res$Responder)` to equal 3.
  Differences:
    `actual`: 0.0
  `expected`: 3.0
  
  ── Failure ('test-core_functions.R:85:1'): test get_multiOmics_diffNetworks multi_omics ──
  Expected `"AKT2" %in% res$Non_responder$from` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-core_functions.R:86:1'): test get_multiOmics_diffNetworks multi_omics ──
  Expected `"MTOR" %in% res$Non_responder$to` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-core_functions.R:88:1'): test get_multiOmics_diffNetworks multi_omics ──
  Expected `"FANCD2" %in% res$Responder$from` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-core_functions.R:89:1'): test get_multiOmics_diffNetworks multi_omics ──
  Expected `"FAN1" %in% res$Responder$to` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Error ('test-plotting_functions.R:19:3'): test get_multiOmics_diffNetworks multi_omics ──
  Error in `do.call(rbind, deggs_object[["diffNetworks"]][[assayDataName]][categories])`: second argument must be a list
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test-plotting_functions.R:19:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─multiDEGGs::plot_regressions(...)
   10.   └─base::do.call(rbind, deggs_object[["diffNetworks"]][[assayDataName]][categories])
  
  [ FAIL 7 | WARN 0 | SKIP 3 | PASS 29 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [7s/11s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘Differential_Network_Analysis.Rmd’ using rmarkdown
--- finished re-building ‘Differential_Network_Analysis.Rmd’

--- re-building ‘Feature_Selection.Rmd’ using rmarkdown

Quitting from Feature_Selection.Rmd:95-117 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'nestedcv'
---
Backtrace:
    ▆
 1. └─base::library(nestedcv)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Feature_Selection.Rmd' failed with diagnostics:
there is no package called 'nestedcv'
--- failed re-building ‘Feature_Selection.Rmd’

SUMMARY: processing the following file failed:
  ‘Feature_Selection.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [9s/11s] 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: 3 ERRORs, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/multiDEGGs.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:08.17, 80.00 + 10.88