add dontrun in examples

R/overlap_coefficient.R

@@ -30,11 +30,13 @@
 #' pathwayB <- "Vitamin digestion and absorption"
 #' overlap_coefficient(pathwayA, pathwayB, pathways)
 #' 
+#' \dontrun{
 #' if (requireNamespace("KEGGREST", quietly = TRUE)) {
 #'   pathwayA <- "Galactose metabolism"
 #'   pathwayB <- "Vitamin digestion and absorption"
 #'   overlap_coefficient(pathwayA, pathwayB, organism = "mmu")
 #' }
+#' }
 #' 
 #' pathwayA <- "mmu00052"
 #' pathwayB <- "mmu00562"

R/pathway_search.R

@@ -17,11 +17,13 @@
 #' @importFrom tidyr separate
 #' 
 #' @examples
+#' \dontrun{
 #' if (requireNamespace("KEGGREST", quietly = TRUE)) {
 #'   data("MTBLS422")
 #'   quantif <- from_ASICS_to_PHOENICS(quantif)
 #'   pathways <- pathway_search(metab = colnames(quantif), organism = "mmu")
 #' }
+#' }
 #' 
 #' @author Camille Guilmineau <camille.guilmineau@inrae.fr>\cr
 #' Remi Servien <remi.servien@inrae.fr>\cr

man/overlap_coefficient.Rd

@@ -44,11 +44,13 @@ pathwayA <- "Galactose metabolism"
 pathwayB <- "Vitamin digestion and absorption"
 overlap_coefficient(pathwayA, pathwayB, pathways)
 
+\dontrun{
 if (requireNamespace("KEGGREST", quietly = TRUE)) {
   pathwayA <- "Galactose metabolism"
   pathwayB <- "Vitamin digestion and absorption"
   overlap_coefficient(pathwayA, pathwayB, organism = "mmu")
 }
+}
 
 pathwayA <- "mmu00052"
 pathwayB <- "mmu00562"
@@ -63,5 +65,5 @@ overlap_coefficient(pathwayA, pathwayB)
 Wieder C., Lai R.P.J., Ebbels T.M.D. (2022). Single sample pathway analysis
 in metabolomics: performance evaluation and application.
 \emph{BMC Bioinformatics}, \strong{23}, 481.
-\url{https://doi.org/10.1186/s12859-022-05005-1}
+\doi{10.1186/s12859-022-05005-1}
 }

man/pathway_search.Rd

@@ -27,17 +27,19 @@ in columns: \itemize{
 Query KEGG pathways for a given set of metabolites
 }
 \examples{
+\dontrun{
 if (requireNamespace("KEGGREST", quietly = TRUE)) {
   data("MTBLS422")
   quantif <- from_ASICS_to_PHOENICS(quantif)
   pathways <- pathway_search(metab = colnames(quantif), organism = "mmu")
 }
+}
 
 }
 \references{
 Kanehisa M., Goto S. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes,
 \emph{Nucleic Acids Research}, Volume 28, Issue 1, Pages 27–30,
-\url{https://doi.org/10.1093/nar/28.1.27}
+\doi{10.1093/nar/28.1.27}
 
 Tenenbaum D., Maintainer B. (2022). KEGGREST: Client-side REST access to the
 Kyoto Encyclopedia of Genes and Genomes (KEGG). R package version 1.38.0.