* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SUMO.Rcheck’
* using R Under development (unstable) (2025-10-13 r88918)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (7)
    Debian flang-new version 19.1.7 (7)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘SUMO/DESCRIPTION’ ... OK
* this is package ‘SUMO’ version ‘1.2.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] 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 whether package ‘SUMO’ can be installed ... [5s/5s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... WARNING
Found the following file with non-ASCII characters:
  R/demo_multiomics_analysis.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.
* 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 ... [9s/9s] 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 ... WARNING
Undocumented arguments in Rd file 'plot_weights.Rd'
  ‘omic’
Documented arguments not in \usage in Rd file 'plot_weights.Rd':
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [2s/2s] ERROR
Running examples in ‘SUMO-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_weights
> ### Title: Visualizing the raw loading/weights of the features
> ### Aliases: plot_weights
> 
> ### ** Examples
> 
> output_obj <- simulate_twoOmicsData(
+   vector_features = c(4000, 3000),
+   n_samples = 100,
+   n_factors = 2,
+   signal.samples = NULL,
+   signal.features.one = NULL,
+   signal.features.two = NULL,
+   snr = 2.5,
+   num.factor = 'multiple',
+   advanced_dist = 'mixed'
+   )
> 
> plot_weights(
+    sim_object = output_obj,
+    factor_num = 1,
+    data = 'omic.one',
+    type = 'scatter',
+    show.legend = FALSE
+    )
Error in plot_weights(sim_object = output_obj, factor_num = 1, data = "omic.one",  : 
  unused argument (data = "omic.one")
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [2s/2s] ERROR
  Running ‘testthat.R’ [2s/2s]
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(SUMO)
  > 
  > test_check("SUMO")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plot_simData.R:17:3'): plot_simData runs without error ─────────
  Error in `plot_simData(sim_object = output_obj, data = "merged", type = "heatmap")`: No omics found in 'sim_object' for merged view.
  Backtrace:
      ▆
   1. ├─testthat::expect_silent(...) at test-plot_simData.R:17:3
   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. └─SUMO::plot_simData(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] NOTE
Found the following HTML validation problems:
sumo_mofa_backend.html:37:16 (sumo_mofa_backend.Rd:12): Error: <conda> is not recognized!
sumo_mofa_backend.html:37:16 (sumo_mofa_backend.Rd:12): Warning: discarding unexpected <conda>
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 2 WARNINGs, 1 NOTE