fixing r cmd check

DESCRIPTION

@@ -1,9 +1,16 @@
 Package: ieugwasr
 Title: R Interface to the OpenGWAS Database API
-Version: 0.1.6
-Authors@R: 
+Version: 0.1.7
+Authors@R: c(
     person("Gibran", "Hemani", , "g.hemani@bristol.ac.uk", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-0920-1055"))
+           comment = c(ORCID = "0000-0003-0920-1055")),
+    person("Ben", "Elsworth", , "Ben.Elsworth@bristol.ac.uk", role = "aut",
+           comment = c(ORCID = "0000-0001-7328-4233")),
+    person("Tom", "Palmer", , "tom.palmer@bristol.ac.uk", role = "aut",
+           comment = c(ORCID = "0000-0003-4655-4511")),
+    person("Rita", "Rasteiro", , "rita.rasteiro@bristol.ac.uk", role = "aut",
+           comment = c(ORCID = "0000-0002-4217-3060"))
+    )
 Description: R interface to the OpenGWAS database API. Includes a wrapper
     to make generic calls to the API, plus convenience functions for
     specific queries.
@@ -30,3 +37,4 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1

R/afl2.r

@@ -39,7 +39,7 @@ afl2_list <- function(variantlist=c("reduced", "hapmap3")[1])
 afl2_rsid <- function(rsid, reference="1000g")
 {
 	out <- api_query("variants/afl2", list(rsid=rsid)) %>% get_query_content()
-	if(class(out) == "response")
+	if(inherits(out, "response"))
 	{
 		return(out)
 	} else if(is.data.frame(out)) {
@@ -60,7 +60,7 @@ afl2_rsid <- function(rsid, reference="1000g")
 afl2_chrpos <- function(chrpos, reference="1000g")
 {
 	out <- api_query("variants/afl2", list(chrpos=chrpos)) %>% get_query_content()
-	if(class(out) == "response")
+	if(inherits(out, "response"))
 	{
 		return(out)
 	} else if(is.data.frame(out)) {

R/api.R

@@ -2,10 +2,11 @@
 #'
 #' @param where Which API to use. Choice between `"public"`, `"private"`, `"dev1"`, `"dev2"`. 
 #' Default = `"public"`.
+#' @param silent Silent? Default = FALSE
 #'
 #' @export
 #' @return NULL
-select_api <- function(where="public")
+select_api <- function(where="public", silent=FALSE)
 {
 	url <- switch(where,
 		public = "http://gwas-api.mrcieu.ac.uk/",
@@ -20,7 +21,9 @@ select_api <- function(where="public")
 	}
 
 	options(ieugwasr_api=url)
-	message("API: ", where, ": ", url)
+	if(!silent) {
+		message("API: ", where, ": ", url)
+	}
 }
 
 

R/query.R

@@ -63,14 +63,14 @@ api_query <- function(path, query=NULL, access_token=check_access_token(),
 				silent=TRUE
 			)			
 		}
-		if('try-error' %in% class(r))
+		if(inherits(r, 'try-error'))
 		{
 			if(grepl("Timeout", as.character(attributes(r)$condition)))
 			{
 				stop("The query to MR-Base exceeded ", timeout, " seconds and timed out. Please simplify the query")
 			}
 		}
-		if(! 'try-error' %in% class(r))
+		if(! inherits(r, 'try-error'))
 		{
 			if(r$status_code >= 500 & r$status_code < 600)
 			{
@@ -94,7 +94,7 @@ api_query <- function(path, query=NULL, access_token=check_access_token(),
 		message("Failed to retrieve results from server. See error status message in the returned object and contact the developers if the problem persists.")
 		return(r)
 	}
-	if('try-error' %in% class(r))
+	if(inherits(r, 'try-error'))
 	{
 		if(grepl("Could not resolve host", as.character(attributes(r)$condition)))
 		{
@@ -145,11 +145,6 @@ api_status <- function()
 	return(o)
 }
 
-print.ApiStatus <- function(x)
-{
-	lapply(names(x), function(y) cat(format(paste0(y, ":"), width=30, justify="right"), x[[y]], "\n"))
-}
-
 
 #' Get list of studies with available GWAS summary statistics through API
 #'
@@ -180,10 +175,6 @@ gwasinfo <- function(id=NULL, access_token = check_access_token())
 	return(out)
 }
 
-print.GwasInfo <- function(x)
-{
-	dplyr::glimpse(x)
-}
 
 #' Extract batch name from study ID
 #'
@@ -246,7 +237,7 @@ associations <- function(variants, id, proxies=1, r2=0.8, align_alleles=1, palin
 		maf_threshold=maf_threshold
 	), access_token=access_token) %>% get_query_content()
 
-	if(class(out) == "response")
+	if(inherits(out, "response"))
 	{
 		return(out)
 	} else if(is.data.frame(out)) {
@@ -316,7 +307,7 @@ phewas <- function(variants, pval = 0.00001, batch=c(), access_token=check_acces
 		pval=pval,
 		index_list=batch
 	), access_token=access_token) %>% get_query_content()
-	if(class(out) != "response")
+	if(!inherits(out, "response"))
 	{
 		out <- out %>% dplyr::as_tibble() %>% fix_n()
 		if(nrow(out) > 0)
@@ -377,7 +368,7 @@ tophits <- function(id, pval=5e-8, clump = 1, r2 = 0.001, kb = 10000, pop="EUR",
 		kb=kb,
 		pop=pop
 	), access_token=access_token) %>% get_query_content()
-	if(class(out) == "response")
+	if(inherits(out, "response"))
 	{
 		return(out)
 	} else if(is.data.frame(out)) {

R/variants.R

@@ -15,7 +15,7 @@ variants_gene <- function(gene, radius=0)
 	{
 		message("Looking up ", gene[i])
 		o <- api_query(paste0('variants/gene/', gene[i], "?radius=", format(radius, scientific=FALSE))) %>% get_query_content()
-		if(class(o) != "response")
+		if(! inherits(o, "response"))
 		{
 			l[[gene[i]]] <- o %>% dplyr::bind_rows() %>% format_variants()
 		}		
@@ -35,7 +35,7 @@ variants_gene <- function(gene, radius=0)
 variants_rsid <- function(rsid)
 {
 	o <- api_query("variants/rsid", list(rsid = rsid)) %>% get_query_content()
-	if(! class(o) %in% "response")
+	if(! inherits(o, "response"))
 	{
 		if(!is.data.frame(o) & is.list(o))
 		{
@@ -62,7 +62,7 @@ variants_chrpos <- function(chrpos, radius=0)
 {
 	o <- api_query("variants/chrpos", list(chrpos = chrpos, radius=radius)) %>% get_query_content() 
 
-	if(! class(o) %in% "response")
+	if(! inherits(o, "response"))
 	{
 		o %>% dplyr::bind_rows() %>% format_variants() %>% return()
 	} else {