Fix lints

Author: arcresu

.lintr

@@ -0,0 +1,9 @@
+encoding: "UTF-8"
+linters: linters_with_defaults(
+    line_length_linter = NULL,
+    object_name_linter = NULL,
+    object_length_linter = NULL,
+    commented_code_linter = NULL,
+    trailing_blank_lines_linter = NULL,
+    trailing_whitespace_linter(allow_empty_lines = TRUE)
+ )

DESCRIPTION

@@ -17,7 +17,6 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Collate: 
     'count.R'
-    'ena.R'
     'process.R'
     'fetch.R'
     'id_set.R'

R/count.R

@@ -1,5 +1,5 @@
 #' Count the number of entries in an ID set
-#' 
+#'
 #' If `id_set` is an [`id_list`] then this is equivalent to `length()`.
 #' If it is a `web_history`, this may involve an Entrez API call to get the
 #' number of entries. In this case the result is cached so that subsequent

R/fetch.R

@@ -1,8 +1,8 @@
 #' Fetch records from Entrez
-#' 
+#'
 #' Fetching can be slow, and Entrez will time out requests that take too long.
 #' This helper supports pagination if you specify `retmax`.
-#' 
+#'
 #' @family API methods
 #' @param id_set ID set object.
 #' @param retstart integer: index of first result (starts from 0).
@@ -65,11 +65,11 @@ efetch <- function(
 }
 
 #' Fetch document summaries from Entrez
-#' 
+#'
 #' ESummary is faster than EFetch because it only interacts with the frontend
 #' rather than the full database. It contains more limited information.
 #' Consider adding `version = "2.0"` to request the revised output format.
-#' 
+#'
 #' @family API methods
 #' @param version character: requested format version.
 #' @inheritParams efetch

R/id_set.R

@@ -2,25 +2,25 @@
 NULL
 
 #' Entrez identifier sets
-#' 
+#'
 #' Many Entrez APIs accept either a UID list or tokens that point to a result stored
 #' on its history server. The classes here wrap these and keep track of the
 #' database name that the identifiers belong to. Most of the API helpers in this
 #' package are generic over the type of ID set and so can be used the same way with
 #' either type. For large numbers of UIDs, the web history versions are generally
 #' recommended to avoid running into server-side request timeouts.
-#' 
+#'
 #' `id_list` is a vector and can be manipulated to take subsets (e.g. `id_set[1:10]` or
 #' `tail(id_set)`).
-#' 
+#'
 #' `web_history` is an opaque reference to an ID list stored on the Entrez
 #' history server. Through the course of API calls, information about the length or
 #' the actual list of IDs may be discovered and cached, avoiding subsequent API calls.
 #' `as_id_list()` can be used to extract the list of IDs.
-#' 
+#'
 #' Convert `id_list` to `web_history` with [`epost()`].
 #' Convert `web_history` to `id_list` with `as_id_list()`.
-#' 
+#'
 #' @rdname id_set
 #' @param db name of the associated Entrez database (e.g. `"biosample"`).
 #' @param ids UIDs, coercible to a character vector (can be accessions or GI numbers).
@@ -192,7 +192,7 @@ check_compatible_db <- function(
 }
 
 #' Check ID set is well formed
-#' 
+#'
 #' @param x ID set object.
 #' @param database name of intended database.
 #'   If `NULL` the database name is not checked.
@@ -217,7 +217,7 @@ check_id_set <- function(
   }
 
   if (!is.null(database)) {
-    actual_db <- entrez_database(x) 
+    actual_db <- entrez_database(x)
     if (database != actual_db) {
       cli::cli_abort(c(
         "{.arg {arg}} is an ID set from the wrong Entrez database",

R/id_set_validate.R

@@ -1,10 +1,10 @@
 #' Look up accessions and other IDs on Entrez
-#' 
+#'
 #' Passes the provided IDs through Entrez which has the effect of normalising the
 #' accepted UIDs, and removing invalid UIDs.
 #' For web history lists, this forces results to be freshly downloaded
 #' (unlike [`as_id_list()`] which can use cached results).
-#' 
+#'
 #' @family API methods
 #' @inheritParams epost
 #' @inheritParams efetch
@@ -43,7 +43,7 @@ as_id_list <- function(x, .paginate = 5000L, .path = NULL, .call = current_env()
 
   ids <- wh_ids_get(x)
   if (is.null(ids)) {
-    res <- download_web_history(x, .paginate = .paginate, .path = .path, .call = .call) 
+    res <- download_web_history(x, .paginate = .paginate, .path = .path, .call = .call)
     ids <- il_ids_get(res)
     wh_ids_set(x, ids)
   }

R/info.R

@@ -1,10 +1,10 @@
 #' Get details about Entrez databases
-#' 
+#'
 #' These functions call the EInfo endpoint. `einfo()` provides the number
 #' of entries in the databases, the name and description, list of terms
 #' usable in the query syntax, and list of link names usable with the ELink
 #' endpoint.
-#' 
+#'
 #' @param db name of database to provide information about.
 #' @param retmode response format.
 #' @param version response format version.

R/jentre-package.R

@@ -1,12 +1,12 @@
 #' jentre: Toolkit for the 'Entrez' API
-#' 
+#'
 #' To use this package effectively, you should have some understanding of
 #' the design of the Entrez API which is documented at
 #' <https://www.ncbi.nlm.nih.gov/books/NBK25500/>.
 #' Helper functions will make it easier to avoid common pitfalls, and to
 #' make use of features like pagination, but you'll still need to understand
 #' how to structure your requests efficiently to avoid undue load.
-#' 
+#'
 #' Entrez API usage is subject to guidelines that are available at the URL above.
 #' Entrez datasets are also subject to copyright. Refer to the NCBI policies at
 #' <https://www.ncbi.nlm.nih.gov/home/about/policies/> for details.

R/link.R

@@ -1,9 +1,9 @@
 #' ELink API for fetching links between databases
-#' 
+#'
 #' `elink()` offers direct access to the ELink API endpoint, which has many different
 #' input and output formats depending on parameters. If you just want a one-to-one
 #' mapping of `neighbor` links, use `elink_map()`, which handles this for you.
-#' 
+#'
 #' @section One-to-one mapping:
 #' Note that some ways of calling this API on multiple UIDs result in the one-to-one
 #' association of the input and output sets getting lost. The way around this is to
@@ -12,7 +12,7 @@
 #' history token as input, there is no corresponding way to ensure one-to-one mapping.
 #' To ensure that the result is always one-to-one, use `elink_map()`, which may make
 #' several API requests to achieve the result.
-#' 
+#'
 #' @family API methods
 #' @inheritParams entrez_request
 #' @param id_set ID set object.

R/post.R

@@ -1,5 +1,5 @@
 #' Register UIDs with the Entrez history server
-#' 
+#'
 #' @param id_set an [`id_list`] object.
 #' @param WebEnv either a character to pass on as-is, or a [`web_history`] object.
 #' @inheritParams entrez_request