• using R Under development (unstable) (2025-10-15 r88920)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 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 ‘DrDimont’ can be installed ... [11s/31s] OK See the install log for details.
• 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 ... [10s/30s] OK
• checking Rd files ... NOTE checkRd: (-1) generate_individual_graphs.Rd:11: Lost braces     11 | code{\link[DrDimont]{compute_correlation_matrices}}}        | ^
• 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 LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [19s/54s] 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))) [25-10-15 19:47:23] 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) [25-10-15 19:47:23] Generating graph of layer mrna for groupA... [25-10-15 19:47:23] Reducing network by WGCNA::pickHardThreshold... [25-10-15 19:47:23] R2 cutoff: 0.65 [25-10-15 19:47:27] 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 ... [34s/91s] 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 ... [12s/35s] 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: 2 ERRORs, 1 NOTE