From 27538ea2ce2178ff3f3802a93297b2c1f0aa14cd Mon Sep 17 00:00:00 2001 From: RonaldVisser <38214052+RonaldVisser@users.noreply.github.com> Date: Sat, 10 Feb 2024 17:50:42 +0100 Subject: [PATCH] dontrun --- NEWS | 2 +- R/clique_community_names_par.R | 2 +- R/cyto_clean_styles.R | 2 +- R/cyto_create_cpm_style.R | 2 +- R/cyto_create_gn_style.R | 2 +- R/cyto_create_graph.R | 2 +- R/wuchswerte.R | 2 +- man/clique_community_names_par.Rd | 2 +- man/cyto_clean_styles.Rd | 2 +- man/cyto_create_cpm_style.Rd | 2 +- man/cyto_create_gn_style.Rd | 2 +- man/cyto_create_graph.Rd | 2 +- man/wuchswerte.Rd | 2 +- 13 files changed, 13 insertions(+), 13 deletions(-) diff --git a/NEWS b/NEWS index 3bd8af6..36cb714 100644 --- a/NEWS +++ b/NEWS @@ -15,7 +15,7 @@ dendroNetwork 0.5.1 (2024-02-10) * added .github/CONTRIBUTING.md using usethis::use_tidy_contributing() * DESCRIPTION: added URL and BugReports to DESCRIPTION + package checks * correction in clique_community_names(_par) functions, due to [k] seen as link - * added \donttest{} to cytoscape functions + * added \dontrun{} to cytoscape functions ### CONTINUOUS INTEGRATION * added GitHub Action for BiocMananager (https://lcolladotor.github.io/biocthis/index.html) * added more tests diff --git a/R/clique_community_names_par.R b/R/clique_community_names_par.R index ba64094..ccea9ca 100644 --- a/R/clique_community_names_par.R +++ b/R/clique_community_names_par.R @@ -10,7 +10,7 @@ #' @returns a dataframe with node names and community name. The community is named as CPM_Kk_number_of_community with k replaced by the value of k. #' #' @examples -#' \donttest{ +#' \dontrun{ #' hol_sim <- sim_table(hol_rom) #' g_hol <- dendro_network(hol_sim, r_threshold = 0.4, sgc_threshold = 0.4) #' clique_community_names_par(g_hol, k = 3, n_core = 2) diff --git a/R/cyto_clean_styles.R b/R/cyto_clean_styles.R index 53cebba..a1ed874 100644 --- a/R/cyto_clean_styles.R +++ b/R/cyto_clean_styles.R @@ -2,7 +2,7 @@ #' #' @returns Cytoscape cleaned of styles and only styles with white and grey nodes. #' @examples -#' \donttest{ +#' \dontrun{ #' cyto_clean_styles() #' } #' diff --git a/R/cyto_create_cpm_style.R b/R/cyto_create_cpm_style.R index 7786b4d..be564e9 100644 --- a/R/cyto_create_cpm_style.R +++ b/R/cyto_create_cpm_style.R @@ -11,7 +11,7 @@ #' @param style_name name of the output style in Cytoscape. If set to "auto", the style is derived from the name of the network and value for k #' @returns The style applied in Cytoscape, no objects in R as return. #' @examples -#' \donttest{ +#' \dontrun{ #' data(hol_rom) #' sim_table_hol <- sim_table(hol_rom) #' g_hol <- dendro_network(sim_table_hol) diff --git a/R/cyto_create_gn_style.R b/R/cyto_create_gn_style.R index 1290621..001ad48 100644 --- a/R/cyto_create_gn_style.R +++ b/R/cyto_create_gn_style.R @@ -9,7 +9,7 @@ #' @param style_name name of the output style in Cytoscape. If set to "auto", the style is derived from the name of the network and value for k #' @returns The style applied in Cytoscape, no objects in R as return. #' @examples -#' \donttest{ +#' \dontrun{ #' data(hol_rom) #' sim_table_hol <- sim_table(hol_rom) #' g_hol <- dendro_network(sim_table_hol) diff --git a/R/cyto_create_graph.R b/R/cyto_create_graph.R index 79c3556..f18a457 100644 --- a/R/cyto_create_graph.R +++ b/R/cyto_create_graph.R @@ -12,7 +12,7 @@ #' #' @returns a graph in Cytoscape #' @examples -#' \donttest{ +#' \dontrun{ #' data(hol_rom) #' sim_table_hol <- sim_table(hol_rom) #' g_hol <- dendro_network(sim_table_hol) diff --git a/R/wuchswerte.R b/R/wuchswerte.R index 992c7e4..1caf5d8 100644 --- a/R/wuchswerte.R +++ b/R/wuchswerte.R @@ -7,7 +7,7 @@ #' @param x tree-ring series #' @returns tree-ring series normalized according to Hollstein (1980, 14-15) #' @examples -#' \donttest{ +#' \dontrun{ #' data(hol_rom) #' wuchswerte(hol_rom) #' # to convert a rwl object into wuchwerte use: diff --git a/man/clique_community_names_par.Rd b/man/clique_community_names_par.Rd index 2df3391..8572d80 100644 --- a/man/clique_community_names_par.Rd +++ b/man/clique_community_names_par.Rd @@ -21,7 +21,7 @@ Function to determine communities in a network using clique percolation method ( This function uses parallelisation and should be used for larger networks. } \examples{ -\donttest{ +\dontrun{ hol_sim <- sim_table(hol_rom) g_hol <- dendro_network(hol_sim, r_threshold = 0.4, sgc_threshold = 0.4) clique_community_names_par(g_hol, k = 3, n_core = 2) diff --git a/man/cyto_clean_styles.Rd b/man/cyto_clean_styles.Rd index eede226..f0c66ed 100644 --- a/man/cyto_clean_styles.Rd +++ b/man/cyto_clean_styles.Rd @@ -13,7 +13,7 @@ Cytoscape cleaned of styles and only styles with white and grey nodes. Cleaning nearly all styles in cytoscape session and import simple styles } \examples{ -\donttest{ +\dontrun{ cyto_clean_styles() } diff --git a/man/cyto_create_cpm_style.Rd b/man/cyto_create_cpm_style.Rd index 5c62a58..f1ad7b7 100644 --- a/man/cyto_create_cpm_style.Rd +++ b/man/cyto_create_cpm_style.Rd @@ -25,7 +25,7 @@ The function uses a graph as input and the number of cliques (default = 3). The Before starting this function, Cytoscape must be up and running! } \examples{ -\donttest{ +\dontrun{ data(hol_rom) sim_table_hol <- sim_table(hol_rom) g_hol <- dendro_network(sim_table_hol) diff --git a/man/cyto_create_gn_style.Rd b/man/cyto_create_gn_style.Rd index 6be5e3f..f8e7af2 100644 --- a/man/cyto_create_gn_style.Rd +++ b/man/cyto_create_gn_style.Rd @@ -22,7 +22,7 @@ Each node is filled with a separate colour for each community. Before starting this function, Cytoscape must be up and running! } \examples{ -\donttest{ +\dontrun{ data(hol_rom) sim_table_hol <- sim_table(hol_rom) g_hol <- dendro_network(sim_table_hol) diff --git a/man/cyto_create_graph.Rd b/man/cyto_create_graph.Rd index 85f82b3..2a1ba7e 100644 --- a/man/cyto_create_graph.Rd +++ b/man/cyto_create_graph.Rd @@ -34,7 +34,7 @@ Function to create a network in cytoscape (https://cytoscape.org/) Cytoscape must be running before executing this function } \examples{ -\donttest{ +\dontrun{ data(hol_rom) sim_table_hol <- sim_table(hol_rom) g_hol <- dendro_network(sim_table_hol) diff --git a/man/wuchswerte.Rd b/man/wuchswerte.Rd index b85e447..f12c908 100644 --- a/man/wuchswerte.Rd +++ b/man/wuchswerte.Rd @@ -19,7 +19,7 @@ Function to normalize tree-ring values according to Hollsteins transformation to Published on pages 14-15 in Hollstein, E. 1980. Mitteleuropäische Eichenchronologie. Trierer Dendrochronologische Forschungen zur Archäologie und Kunstgeschichte. Trierer Grabungen und Forschungen 11. Mainz am Rhein: Verlag Philipp von Zabern. } \examples{ -\donttest{ +\dontrun{ data(hol_rom) wuchswerte(hol_rom) # to convert a rwl object into wuchwerte use: