* using log directory 'd:/Rcompile/CRANpkg/local/4.5/DrDimont.Rcheck'
* using R version 4.5.2 (2025-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'DrDimont/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DrDimont' version '0.1.4'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'DrDimont' can be installed ... OK
* checking installed package size ... 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 ... [0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [0s] 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 ... [4s] OK
* checking Rd files ... [1s] NOTE
checkRd: (-1) generate_individual_graphs.Rd:11: Lost braces
    11 | code{\link[DrDimont]{compute_correlation_matrices}}}
       |     ^
* checking Rd metadata ... 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 ... [1s] 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 ... [12s] ERROR
Running examples in 'DrDimont-Ex.R' failed
The error most likely occurred in:

> ### Name: generate_individual_graphs
> ### Title: Builds graphs from specified network layers
> ### Aliases: generate_individual_graphs
> 
> ### ** Examples
> 
> ## Don't show: 
> WGCNA::disableWGCNAThreads()
> ## End(Don't show)
> 
> data(layers_example)
> data(correlation_matrices_example)
> 
> example_settings <- drdimont_settings(
+                         handling_missing_data=list(
+                             default="pairwise.complete.obs",
+                             mrna="all.obs"),
+                         reduction_method="pickHardThreshold",
+                         r_squared=list(default=0.65, metabolite=0.1),
+                         cut_vector=list(default=seq(0.2, 0.5, 0.01)))
[25-11-01 06:12:07] WARNING: Python executable in virtual environment 'r-DrDimont' not found. Either run `install_python_dependencies(package_manager='pip') or set `conda=TRUE` in `drdimont_settings()` if conda installation was used.
> 
> example_individual_graphs <- generate_individual_graphs(
+                                  correlation_matrices=correlation_matrices_example,
+                                  layers=layers_example, 
+                                  settings=example_settings)
[25-11-01 06:12:07] Generating graph of layer mrna for groupA...
[25-11-01 06:12:07] Reducing network by WGCNA::pickHardThreshold...
[25-11-01 06:12:07] R2 cutoff: 0.65
[25-11-01 06:12:08] Cut Threshold: 0.26
Error in `graph_from_adjacency_matrix()`:
! Cannot create a graph object because the adjacency matrix contains
  NAs.
Backtrace:
    ▆
 1. └─DrDimont::generate_individual_graphs(...)
 2.   └─DrDimont::generate_reduced_graph(...)
 3.     └─igraph::graph.adjacency(...)
 4.       └─igraph::graph_from_adjacency_matrix(...)
 5.         └─igraph:::ensure_no_na(adjmatrix, "adjacency matrix")
 6.           └─cli::cli_abort(...)
 7.             └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [10s] ERROR
Error(s) in re-building vignettes:
--- re-building 'DrDimont_Vignette.Rmd' using rmarkdown

Quitting from DrDimont_Vignette.Rmd:327-333 [Individual graphs]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DrDimont_Vignette.Rmd' failed with diagnostics:
Cannot create a graph object because the adjacency matrix contains NAs.
--- failed re-building 'DrDimont_Vignette.Rmd'

SUMMARY: processing the following file failed:
  'DrDimont_Vignette.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [27s] OK
* checking HTML version of manual ... [9s] OK
* DONE
Status: 2 ERRORs, 1 NOTE