Changed examples from dontrun to donttest

R/allgensnp.R

@@ -6,7 +6,7 @@
 #' @param usersubset Get a subset of users, integer numbers, e.g. 1-8 (default: none)
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return data.frame of genotypes for all users at a certain SNP
-#' @examples \dontrun{
+#' @examples \donttest{
 #' x <- allgensnp(snp = "rs7412")
 #' head(x)
 #' }

R/allphenotypes.R

@@ -12,7 +12,7 @@
 #' number_of_users are replicated in the data.frame. Default: `FALSE`
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return data.frame of results, or list if `df=FALSE`
-#' @examples \dontrun{
+#' @examples \donttest{
 #' # Get all data
 #' allphenotypes(df = TRUE)
 #'

R/annotations.R

@@ -13,7 +13,7 @@
 #' 		metadata for the response.
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return data.frame of results
-#' @examples \dontrun{
+#' @examples \donttest{
 #' # Get all data
 #' ## get just the metadata
 #' annotations(snp = "rs7903146", output = "metadata")

R/download_users.R

@@ -65,10 +65,10 @@ get_write <- function(x, y, ...) {
 #' variables for the path to the file saved. Alternatively, you can supply
 #' the path.
 #' @return A data.frame.
-#' @examples \dontrun{
-#' # dat <- read_users(name = "kevinmcc")
-#' # head(dat)
-#' # dat <- read_users(id = 285)
+#' @examples \donttest{
+#' dat <- read_users(name = "kevinmcc")
+#' head(dat)
+#' dat <- read_users(id = 285)
 #' }
 read_users <- function(name = NULL, id = NULL, path = NULL, ...) {
   if (is.null(name) && is.null(id) && is.null(path)) {

R/fetch_genotypes.R

@@ -28,7 +28,7 @@
 #' Internally, we use [download.file()] to download each file, then
 #' [read.table()] to read the file to a data.frame.
 #'
-#' @examples \dontrun{
+#' @examples \donttest{
 #' # get a data.frame of the users data
 #' data <- users(df = TRUE)
 #' head(data[[1]]) # users with links to genome data

R/genotypes.R

@@ -8,7 +8,7 @@
 #' @param ... Curl options passed on to [crul::HttpClient]]
 #' @return List (or data.frame) of genotypes for specified user(s) at a
 #' certain SNP.
-#' @examples \dontrun{
+#' @examples \donttest{
 #' genotypes(snp = "rs9939609", userid = 1)
 #' genotypes("rs9939609", userid = "1,6,8", df = TRUE)
 #' genotypes("rs9939609", userid = "1-2", df = FALSE)

R/ncbi_snp_api.R

@@ -211,7 +211,7 @@ get_gene_names <- function(primary_info) {
 #' If users want to set curl options when querying for the SNPs they can do so by using
 #'  httr::set_config/httr::with_config
 #'
-#' @examples \dontrun{
+#' @examples \donttest{
 #' ## an example with both merged SNPs, non-SNV SNPs, regular SNPs,
 #' ## SNPs not found, microsatellite
 #' SNPs <- c("rs332", "rs420358", "rs1837253", "rs1209415715", "rs111068718")

R/phenotypes.R

@@ -7,7 +7,7 @@
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return List of phenotypes for specified user(s).
 #'
-#' @examples \dontrun{
+#' @examples \donttest{
 #' phenotypes(userid = 1)
 #' phenotypes(userid = "1,6,8", df = TRUE)
 #' phenotypes(userid = "1-8", df = TRUE)

R/phenotypes_byid.R

@@ -9,7 +9,7 @@
 #' @return List of description of phenotype, list of known variants, or
 #' data.frame of variants for each user with that phenotype.
 #'
-#' @examples \dontrun{
+#' @examples \donttest{
 #' phenotypes_byid(phenotypeid = 12, return_ = "desc")
 #' phenotypes_byid(phenotypeid = 12, return_ = "knownvars")
 #' phenotypes_byid(phenotypeid = 12, return_ = "users")

R/users.R

@@ -5,7 +5,7 @@
 #' @param df Return data.frame (`TRUE`) or not (`FALSE`). Default: `FALSE`
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return List of openSNP users, their ID numbers, and XX if available.
-#' @examples \dontrun{
+#' @examples \donttest{
 #' # just the list
 #' data <- users(df = FALSE)
 #' data