Last updated on 2025-10-24 12:50:47 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| DrDimont | 8 | 5 | |
| LoopDetectR | 13 |
Current CRAN status: ERROR: 8, NOTE: 5
Version: 0.1.4
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Katharina Baum <katharina.baum@hpi.de>’
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
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-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-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)))
[25-10-23 16:59:45] 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)
[25-10-23 16:59:45] Generating graph of layer mrna for groupA...
[25-10-23 16:59:45] Reducing network by WGCNA::pickHardThreshold...
[25-10-23 16:59:45] R2 cutoff: 0.65
[25-10-23 16:59:46] 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 7.822 0.485 12.009
Flavor: r-devel-linux-x86_64-debian-clang
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-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, 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)))
[25-10-23 13:02:16] 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)
[25-10-23 13:02:16] Generating graph of layer mrna for groupA...
[25-10-23 13:02:16] Reducing network by WGCNA::pickHardThreshold...
[25-10-23 13:02:16] R2 cutoff: 0.65
[25-10-23 13:02:17] 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 4.907 0.394 6.009
Flavor: r-devel-linux-x86_64-debian-gcc
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)))
[25-10-22 12:36:18] 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)
[25-10-22 12:36:18] Generating graph of layer mrna for groupA...
[25-10-22 12:36:18] Reducing network by WGCNA::pickHardThreshold...
[25-10-22 12:36:18] R2 cutoff: 0.65
[25-10-22 12:36:20] 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-devel-linux-x86_64-fedora-clang
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-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-windows-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)))
[25-10-20 19:09:38] 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)
[25-10-20 19:09:38] Generating graph of layer mrna for groupA...
[25-10-20 19:09:38] Reducing network by WGCNA::pickHardThreshold...
[25-10-20 19:09:38] R2 cutoff: 0.65
[25-10-20 19:09:41] 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-devel-linux-x86_64-fedora-gcc
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)))
[25-10-14 07:20:12] 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)
[25-10-14 07:20:12] Generating graph of layer mrna for groupA...
[25-10-14 07:20:12] Reducing network by WGCNA::pickHardThreshold...
[25-10-14 07:20:12] R2 cutoff: 0.65
[25-10-14 07:20:12] 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-devel-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)))
[25-10-22 05:10:12] 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)
[25-10-22 05:10:12] Generating graph of layer mrna for groupA...
[25-10-22 05:10:12] Reducing network by WGCNA::pickHardThreshold...
[25-10-22 05:10:12] R2 cutoff: 0.65
[25-10-22 05:10:13] 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 7.766 0.302 11.336
Flavor: r-patched-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)))
[25-10-18 04:58:39] 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)
[25-10-18 04:58:39] Generating graph of layer mrna for groupA...
[25-10-18 04:58:39] Reducing network by WGCNA::pickHardThreshold...
[25-10-18 04:58:39] R2 cutoff: 0.65
[25-10-18 04:58:40] 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 7.63 0.497 11.409
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)))
[25-10-22 03:10:37] 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)
[25-10-22 03:10:37] Generating graph of layer mrna for groupA...
[25-10-22 03:10:37] Reducing network by WGCNA::pickHardThreshold...
[25-10-22 03:10:37] R2 cutoff: 0.65
[25-10-22 03:10:38] 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
Flavor: r-oldrel-windows-x86_64
Current CRAN status: OK: 13