Validation Report - ClustAssess@1.0.0
Context
This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:
- Installation environment description
- Testing coverage
It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.
Package ClustAssess
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 56 |
| has_vignettes | 0 |
| export_help | 56 |
| has_website | TRUE |
| has_maintainer | Andi Munteanu am3019@cam.ac.uk |
| bugs_status | subscript out of bounds |
| has_source_control | https://github.com/Core-Bioinformatics/ClustAssess |
| has_bug_reports_url | 1 |
| downloads_1yr | 3401 |
| reverse_dependencies | 0 |
| has_examples | 0.983871 |
| dependencies | 37 |
| license | MIT + file LICENSE |
Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.
Dependencies
Overall the package has these dependencies:
| package | type | |
|---|---|---|
| 1 | methods | Depends |
| 2 | stats | Depends |
| 3 | dplyr | Imports |
| 4 | DT | Imports |
| 5 | fastcluster | Imports |
| 6 | foreach | Imports |
| 7 | glue | Imports |
| 8 | Gmedian | Imports |
| 9 | ggnewscale | Imports |
| 10 | ggplot2 | Imports |
| 11 | ggrastr | Imports |
| 12 | ggrepel | Imports |
| 13 | ggtext | Imports |
| 14 | gprofiler2 | Imports |
| 15 | igraph | Imports |
| 16 | jsonlite | Imports |
| 17 | leiden | Imports |
| 18 | Matrix (>= 1.5.0) | Imports |
| 19 | matrixStats | Imports |
| 20 | progress | Imports |
| 21 | stringr | Imports |
| 22 | paletteer | Imports |
| 23 | plotly | Imports |
| 24 | qualpalr | Imports |
| 25 | RANN | Imports |
| 26 | reshape2 | Imports |
| 27 | rlang | Imports |
| 28 | Seurat | Imports |
| 29 | shiny | Imports |
| 30 | shinyjs | Imports |
| 31 | shinyLP | Imports |
| 32 | shinyWidgets | Imports |
| 33 | utils | Imports |
| 34 | uwot | Imports |
| 35 | vioplot | Imports |
| 36 | Rcpp | LinkingTo |
| 37 | RcppEigen | LinkingTo |
Package dependencies
Reverse dependencies
Overall the package has 0 reverse dependencies:
Namespace
Overall the package has 56 exported objects. 56 are documented:
add_metadata
TRUE
assess_clustering_stability
TRUE
assess_feature_stability
TRUE
assess_nn_stability
TRUE
automatic_stability_assessment
TRUE
calculate_markers
TRUE
calculate_markers_shiny
TRUE
choose_stable_clusters
TRUE
consensus_cluster
TRUE
create_monocle_default
TRUE
create_monocle_from_clustassess
TRUE
create_monocle_from_clustassess_app
TRUE
create_seurat_object_default
TRUE
create_seurat_object_from_clustassess_app
TRUE
element_agreement
TRUE
element_consistency
TRUE
element_sim
TRUE
element_sim_elscore
TRUE
element_sim_matrix
TRUE
get_clusters_from_clustassess_object
TRUE
get_highest_prune_param
TRUE
get_highest_prune_param_embedding
TRUE
get_nn_conn_comps
TRUE
getNNmatrix
TRUE
marker_overlap
TRUE
merge_partitions
TRUE
pac_convergence
TRUE
pac_landscape
TRUE
plot_clustering_overall_stability
TRUE
plot_clustering_per_value_stability
TRUE
plot_connected_comps_evolution
TRUE
plot_feature_overall_stability_boxplot
TRUE
plot_feature_overall_stability_incremental
TRUE
plot_feature_per_resolution_stability_boxplot
TRUE
plot_feature_per_resolution_stability_incremental
TRUE
plot_feature_stability_ecs_facet
TRUE
plot_feature_stability_mb_facet
TRUE
plot_k_n_partitions
TRUE
plot_k_resolution_corresp
TRUE
plot_n_neigh_ecs
TRUE
plot_n_neigh_k_correspondence
TRUE
server_comparisons
TRUE
server_dimensionality_reduction
TRUE
server_graph_clustering
TRUE
server_graph_construction
TRUE
server_landing_page
TRUE
server_sandbox
TRUE
ui_comparisons
TRUE
ui_dimensionality_reduction
TRUE
ui_graph_clustering
TRUE
ui_graph_construction
TRUE
ui_landing_page
TRUE
ui_sandbox
TRUE
weighted_element_consistency
TRUE
write_objects
TRUE
write_shiny_app
TRUE Examples
There are 61 help pages with examples, from 62 (98.39 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
Installation environment
System Info
| Field | Value |
|---|---|
| Image | rhub/ref-image |
| OS | Ubuntu 24.04.1 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-02-16 04:37:41 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
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[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.49 jsonlite_1.8.9
[10] xfun_0.50 digest_0.6.37 rlang_1.1.5
[13] evaluate_1.0.3 Platform used:
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TRUE TRUE TRUE TRUE FALSE FALSE
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BLAS
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-1.638200e+04 1.638400e+04 Random number generation process:
[1] "Mersenne-Twister" "Inversion" "Rejection" Information about the environment
Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report
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