Merge pull request #177 from ropensci/T171_donttest

Changed examples from dontrun to using examplesif so that they do not run on cran

R/allgensnp.R

@@ -6,10 +6,9 @@
 #' @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{
+#' @examplesIf !rsnps:::is_rcmd_check()
 #' x <- allgensnp(snp = "rs7412")
 #' head(x)
-#' }
 allgensnp <- function(snp = NA, usersubset = FALSE, ...) {
   ## add possibilty to get a subset of users
 

R/allphenotypes.R

@@ -12,17 +12,13 @@
 #' number_of_users are replicated in the data.frame. Default: `FALSE`
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return data.frame of openSNP phenotypes, variants and users per phenotype, or list if `df=FALSE`
-#' @examples \dontrun{
-#' # Get all data
-#' allphenotypes(df = TRUE)
-#'
+#' @examplesIf !rsnps:::is_rcmd_check()
 #' # Output a list, then call the characteristic of interest by 'id' or
-#' # 'characteristic'
+#'  'characteristic'
 #' datalist <- allphenotypes()
 #' names(datalist) # get list of all characteristics you can call
 #' datalist[["ADHD"]] # get data.frame for 'ADHD'
 #' datalist[c("mouth size", "SAT Writing")] # get data.frame for 'ADHD'
-#' }
 allphenotypes <- function(df = FALSE, ...) {
   tryCatch(
     {

R/annotations.R

@@ -13,7 +13,7 @@
 #' 		metadata for the response.
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return data.frame of openSNP phenotypes from specified source
-#' @examples \dontrun{
+#' @examplesIf !rsnps:::is_rcmd_check()
 #' # Get all data
 #' ## get just the metadata
 #' annotations(snp = "rs7903146", output = "metadata")
@@ -26,7 +26,7 @@
 #'
 #' ## get all annotations
 #' annotations(snp = "rs7903146", output = "all")
-#' }
+
 annotations <- function(snp = NA,
                         output = c("all", "plos", "mendeley", "snpedia", "metadata"), ...) {
   url <- paste0(osnp_base(), "snps/json/annotation/", snp, ".json")

R/download_users.R

@@ -8,17 +8,13 @@
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return File downloaded to directory you specify (or default), nothing
 #' returned in R.
-#' @examples \dontrun{
+#' @examplesIf !rsnps:::is_rcmd_check()
 #' # Download a single user file, by id
 #' download_users(id = 14)
 #'
 #' # Download a single user file, by user name
 #' download_users(name = "kevinmcc")
-#'
-#' # Download many user files
-#' lapply(c(14, 22), function(x) download_users(id = x))
-#' read_users(id = 14, nrows = 5)
-#' }
+
 download_users <- function(name = NULL, id = NULL, dir = "~/", ...) {
   if (is.null(name) && is.null(id)) {
     stop("You must specify one of name or id", call. = FALSE)
@@ -65,11 +61,12 @@ get_write <- function(x, y, ...) {
 #' variables for the path to the file saved. Alternatively, you can supply
 #' the path.
 #' @return A data.frame with openSNP user files retrieved from local storage
-#' @examples \dontrun{
+#' @examplesIf !rsnps:::is_rcmd_check()
+#' 
+#' download_users(name = "kevinmcc")
 #' 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)) {
     stop("You must specify one of name, id, or path", call. = FALSE)

R/fetch_genotypes.R

@@ -28,10 +28,9 @@
 #' Internally, we use [download.file()] to download each file, then
 #' [read.table()] to read the file to a data.frame.
 #'
-#' @examples \dontrun{
+#' @examplesIf !rsnps:::is_rcmd_check()
 #' # get a data.frame of the users data
 #' data <- users(df = TRUE)
-#' head(data[[1]]) # users with links to genome data
 #' mydata <- fetch_genotypes(
 #'   url = data[[1]][1, "genotypes.download_url"],
 #'   file = "~/myfile.txt"
@@ -42,7 +41,6 @@
 #'
 #' # Or read in data later separately
 #' read.table("~/myfile.txt", nrows = 10)
-#' }
 fetch_genotypes <- function(url, rows = 100, filepath = NULL, quiet = TRUE, ...) {
   if (is.null(filepath)) filepath <- tempfile(fileext = ".txt")
 

R/genotypes.R

@@ -8,11 +8,10 @@
 #' @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{
+#' @examplesIf !rsnps:::is_rcmd_check()
 #' genotypes(snp = "rs9939609", userid = 1)
 #' genotypes("rs9939609", userid = "1,6,8", df = TRUE)
 #' genotypes("rs9939609", userid = "1-2", df = FALSE)
-#' }
 genotypes <- function(snp = NA, userid = NA, df = FALSE, ...) {
   url2 <- paste0(paste0(osnp_base(), "snps/json/"), snp, "/", userid, ".json")
 

R/ncbi_snp_api.R

@@ -211,23 +211,21 @@ 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{
+#' @examplesIf !rsnps:::is_rcmd_check()
 #' ## an example with both merged SNPs, non-SNV SNPs, regular SNPs,
 #' ## SNPs not found, microsatellite
 #' SNPs <- c("rs332", "rs420358", "rs1837253", "rs1209415715", "rs111068718")
 #' ncbi_snp_query(SNPs)
 #' # ncbi_snp_query("123456") ##invalid: must prefix with 'rs'
 #' ncbi_snp_query("rs420358")
-#' ncbi_snp_query("rs332") # warning that its merged into another, try that
+#' ncbi_snp_query("rs332") # warning that its merged into another
 #' ncbi_snp_query("rs121909001")
 #' ncbi_snp_query("rs1837253")
 #' ncbi_snp_query("rs1209415715")
 #' ncbi_snp_query("rs111068718")
 #' ncbi_snp_query(snps = "rs9970807")
 #'
 #' ncbi_snp_query("rs121909001")
-#' ncbi_snp_query("rs121909001", verbose = TRUE)
-#' }
 ncbi_snp_query <- function(snps) {
 
   ## NCBI moved to https but not using http v.2. The setting of the version

R/phenotypes.R

@@ -7,20 +7,13 @@
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return List of phenotypes for specified user(s) from openSNP.
 #'
-#' @examples \dontrun{
+#' @examplesIf !rsnps:::is_rcmd_check()
 #' phenotypes(userid = 1)
 #' phenotypes(userid = "1,6,8", df = TRUE)
 #' phenotypes(userid = "1-8", df = TRUE)
 #'
-#' # coerce to data.frame
-#' library(plyr)
-#' df <- ldply(phenotypes(userid = "1-8", df = TRUE))
-#' head(df)
-#' tail(df)
-#'
 #' # pass on curl options
 #' phenotypes(1, verbose = TRUE)
-#' }
 phenotypes <- function(userid = NA, df = FALSE, ...) {
   url2 <- paste0(paste0(osnp_base(), "phenotypes/json/"), userid, ".json")
 

R/phenotypes_byid.R

@@ -8,15 +8,13 @@
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return List of description of phenotype, list of known variants, or
 #' data.frame of variants for each user with that phenotype retrieved from openSNP.
-#'
-#' @examples \dontrun{
+#' @examplesIf !rsnps:::is_rcmd_check()
 #' phenotypes_byid(phenotypeid = 12, return_ = "desc")
 #' phenotypes_byid(phenotypeid = 12, return_ = "knownvars")
 #' phenotypes_byid(phenotypeid = 12, return_ = "users")
 #'
 #' # pass on curl options
 #' phenotypes_byid(phenotypeid = 12, return_ = "desc", verbose = TRUE)
-#' }
 phenotypes_byid <- function(phenotypeid = NA,
                             return_ = c("description", "knownvars", "users"), ...) {
   url2 <- paste0(

R/users.R

@@ -5,16 +5,11 @@
 #' @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 genome data if available.
-#' @examples \dontrun{
-#' # just the list
-#' data <- users(df = FALSE)
-#' data
-#'
+#' @examplesIf !rsnps:::is_rcmd_check()
 #' # get a data.frame of the users data
 #' data <- users(df = TRUE)
 #' data[[1]] # users with links to genome data
 #' data[[2]] # users without links to genome data
-#' }
 users <- function(df = FALSE, ...) {
 
 

R/utils.R

@@ -114,3 +114,11 @@ release_bullets <- function() {
     "Bump dev version"
   )
 }
+
+is_rcmd_check <- function () {
+  if (identical(Sys.getenv("NOT_CRAN"), "true")) {
+    FALSE
+  } else {
+    Sys.getenv("_R_CHECK_PACKAGE_NAME_", "") != ""
+  }
+}