fix cmd check issues

Author: grlloyd

DESCRIPTION

@@ -68,6 +68,7 @@ Collate:
     'calc_rt_diff_class.R'
     'lcms_table_class.R'
     'cd_source_class.R'
+    'chart_plot_doc.R'
     'rest_api_parsers.R'
     'rest_api_class.R'
     'classyfire_lookup_class.R'
@@ -94,6 +95,7 @@ Collate:
     'kegg_lookup_class.R'
     'lipidmaps_lookup_class.R'
     'ls_source_class.R'
+    'model_apply_doc.R'
     'mspurity_source_class.R'
     'mwb_compound_lookup_class.R'
     'mwb_refmet_database_class.R'

LICENSE

@@ -98,7 +98,6 @@ exportMethods(model_apply)
 exportMethods(read_database)
 exportMethods(read_source)
 exportMethods(required_cols)
-exportMethods(show)
 exportMethods(vertical_join)
 exportMethods(write_database)
 import(cowplot, except = theme_map)
@@ -110,6 +109,7 @@ import(methods)
 import(rlang)
 import(struct)
 importFrom(scales,manual_pal)
+importFrom(stats,setNames)
 importFrom(utils,URLencode)
 importFrom(utils,capture.output)
 importFrom(utils,modifyList)

NAMESPACE

@@ -54,6 +54,7 @@ AnnotationDb_database <- function(
 )
 
 #' @export
+#' @rdname read_database
 setMethod(
     f = "read_database",
     signature = c("AnnotationDb_database"), definition = function(obj) {

R/AnnotationDb_database.R

@@ -116,8 +116,8 @@ AnnotationDb_select <- function(
 )
 
 
-
 #' @export
+#' @template model_apply
 setMethod(
     f = "model_apply",
     signature = c("AnnotationDb_select", "annotation_source"),

R/AnnotationDb_select_class.R

@@ -111,6 +111,7 @@ BiocFileCache_database <- function(
 )
 
 #' @export
+#' @rdname read_database
 setMethod(
     f = "read_database",
     signature = c("BiocFileCache_database"),

R/BiocFileCache_database_class.R

@@ -23,7 +23,7 @@
 #' @return TRUE if successful
 #' @examples
 #' M <- BiocFileCache_database(
-#'     path = tempfile(),
+#'     source = tempfile(),
 #'     resource_name = "example",
 #'     bfc_fun = .unzip
 #' )
@@ -49,7 +49,7 @@
 #' @return TRUE if successful
 #' @examples
 #' M <- BiocFileCache_database(
-#'     path = tempfile(),
+#'     source = tempfile(),
 #'     resource_name = "example",
 #'     bfc_fun = .cache_as_is
 #' )

R/BiocFileCache_database_helpers.R

@@ -28,6 +28,7 @@ CompoundDb_source <- function(
 )
 
 #' @export
+#' @template model_apply
 setMethod(
     f = "model_apply",
     signature = c("CompoundDb_source", "annotation_source"),

R/CompoundDb_source_class.R

@@ -57,9 +57,9 @@ MTox700plus_database <- function(
             name = "MTox700+ version number",
             description = paste0(
                 "The version number of the MTox700+ database to import. ",
-                "Available versions are listed here: ",
-                '[https://github.com/michabohealthscience/MTox700plus/',
-                'releases].',
+                "Available versions are listed ",
+                '\\href{https://github.com/michabohealthscience/MTox700plus/',
+                'releases}{here}.',
                 ' `version` should match the tag of the release e.g. `"v1.0"`.',
                 ' For convenience `version = "latest"` will always retrieve ',
                 "the most recent release. To prevent unecessary downloads ",
@@ -84,6 +84,7 @@ MTox700plus_database <- function(
 
 
 #' @export
+#' @rdname read_database
 setMethod(
     f = "read_database",
     signature = c("MTox700plus_database"), definition = function(obj) {

R/MTox700plus_database_class.R

@@ -1,5 +1,6 @@
 #' @import struct
 #' @importFrom utils URLencode modifyList read.csv stack unzip
+#' @importFrom stats setNames
 #' @keywords internal
 "_PACKAGE"