up

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MGnifyR
 Type: Package
-Version: 0.99.28
+Version: 0.99.29
 Authors@R:
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",
@@ -16,7 +16,7 @@ Description:
     in R. The package can be used to import microbial data for instance into
     TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly
     compatible with miaverse framework.
-biocViews: Software, Infrastructure, DataImport, MicrobiomeData, SequencingData, Metagenomics
+biocViews: Infrastructure, DataImport, Metagenomics
 License: Artistic-2.0 | file LICENSE
 Encoding: UTF-8
 Depends:

R/deprecate.R

@@ -53,7 +53,9 @@
 #' @param complete_url -
 #'
 #' @param qopts -
-#'
+#' 
+#' @return -
+#' 
 #' @name deprecate
 NULL
 
@@ -124,7 +126,7 @@ mgnify_download <- function(
 #' @rdname deprecate
 #' @export
 mgnify_get_analyses_results <- function(
-        client  =NULL, accessions, retrievelist = c(), compact_results = TRUE,
+        client  = NULL, accessions, retrievelist = c(), compact_results = TRUE,
         usecache = TRUE, bulk_dl = FALSE, ...){
     .Deprecated("getResult")
     if( length(retrievelist) == 0 ){
@@ -162,7 +164,7 @@ mgnify_get_analyses_metadata <- function(
 #' @export
 mgnify_retrieve_json <- function(
         client, path = "biomes", complete_url = NULL, qopts = NULL,
-        maxhits = 200, usecache = FALSE, Debug = FALSE){
+        maxhits = 200, usecache = FALSE, Debug = FALSE, ...){
     .Deprecated(msg = "'mgnify_retrieve_json' is deprecated.\n",
                 "See other functions and use them instead.\n",
                 "See help('Deprecated')")

R/getFile.R

@@ -107,7 +107,7 @@ setMethod("getFile", signature = c(x = "MgnifyClient"), function(
 #' single data.frame containing all available downloads and associated
 #' metadata, including the url location and description. This can then be
 #' filtered to extract the urls of interest, before actually
-#' retrieving the files using \code{mgnify_download}
+#' retrieving the files using \code{fetFile()}
 #'
 #' @param accession A single character value or a vector of character values
 #' specifying accession IDs to return results for.