* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/DrDimont.Rcheck’ * using R Under development (unstable) (2025-10-15 r88920) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * 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 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 ... 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 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 ... 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 ... 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 22:25:46] 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 22:25:46] Generating graph of layer mrna for groupA... [25-10-15 22:25:46] Reducing network by WGCNA::pickHardThreshold... [25-10-15 22:25:46] R2 cutoff: 0.65 [25-10-15 22:25:47] 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 examples with --run-donttest ... 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 22:25:55] 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 22:25:55] Generating graph of layer mrna for groupA... [25-10-15 22:25:55] Reducing network by WGCNA::pickHardThreshold... [25-10-15 22:25:55] R2 cutoff: 0.65 [25-10-15 22:25:56] 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 ... [16s/16s] 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 ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 3 ERRORs, 1 NOTE See ‘/data/blackswan/ripley/R/packages/tests-devel/DrDimont.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:41.09, 94.00 + 66.20