CRAN Package Check Results for Maintainer ‘Katharina Baum <katharina.baum at fu-berlin.de>’

Last updated on 2025-11-11 15:51:10 CET.

Package	ERROR	OK
DrDimont	3	10

Package DrDimont

Current CRAN status: ERROR: 3, OK: 10

Version: 0.1.4
Check: Rd files
Result: NOTE checkRd: (-1) generate_individual_graphs.Rd:11: Lost braces 11 | code{\link[DrDimont]{compute_correlation_matrices}}} | ^ Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64

Version: 0.1.4
Check: examples
Result: ERROR Running examples in ‘DrDimont-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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))) [25-11-05 05:09:37] 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) [25-11-05 05:09:37] Generating graph of layer mrna for groupA... [25-11-05 05:09:37] Reducing network by WGCNA::pickHardThreshold... [25-11-05 05:09:37] R2 cutoff: 0.65 [25-11-05 05:09:38] 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed compute_correlation_matrices 7.555 0.392 9.271 Flavor: r-patched-linux-x86_64

Version: 0.1.4
Check: re-building of vignette outputs
Result: 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 Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.1.4
Check: examples
Result: ERROR Running examples in ‘DrDimont-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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))) [25-11-08 04:58:29] 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) [25-11-08 04:58:29] Generating graph of layer mrna for groupA... [25-11-08 04:58:29] Reducing network by WGCNA::pickHardThreshold... [25-11-08 04:58:29] R2 cutoff: 0.65 [25-11-08 04:58:30] 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed compute_correlation_matrices 7.423 0.348 9.089 Flavor: r-release-linux-x86_64

Version: 0.1.4
Check: examples
Result: 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))) [25-11-08 06:43:44] 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) [25-11-08 06:43:44] Generating graph of layer mrna for groupA... [25-11-08 06:43:44] Reducing network by WGCNA::pickHardThreshold... [25-11-08 06:43:44] R2 cutoff: 0.65 [25-11-08 06:43:45] 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 Flavor: r-release-windows-x86_64

Version: 0.1.4
Check: re-building of vignette outputs
Result: 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 Flavor: r-release-windows-x86_64