fix cmd check issues

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'

NAMESPACE

@@ -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)

R/AnnotationDb_database.R

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

R/AnnotationDb_select_class.R

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

R/BiocFileCache_database_class.R

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

R/BiocFileCache_database_helpers.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/CompoundDb_source_class.R

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

R/MTox700plus_database_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/MetMashR-package.R

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

R/PathBank_metabolite_database_class.R

@@ -40,7 +40,7 @@ PathBank_metabolite_database <- function(
                     " Hasan and Pon, Allison and Budinski, Zachary and ",
                     "Patron, ",
                     "Jonas and Lipton, Debra and Cao, Xuan and Oler, Eponine ",
-                    "and Li, Krissa and Paccoud, Maïlys and Hong, Chelsea and ",
+                    "and Li, Krissa and Paccoud, Ma\u00EFlys and Hong, Chelsea and ",
                     "Guo, An C and Chan, Christopher and Wei, William and ",
                     "Ramirez-Gaona, Miguel"
                 )),
@@ -91,6 +91,7 @@ PathBank_metabolite_database <- function(
 
 
 #' @export
+#' @rdname read_database
 setMethod(
     f = "read_database",
     signature = c("PathBank_metabolite_database"), definition = function(obj) {

R/add_columns_class.R

@@ -3,12 +3,18 @@
 #' @include annotation_source_class.R
 #' @seealso [dplyr::left_join()]
 add_columns <- function(new_columns, by, ...) {
+
+    if (nrow(new_columns)==0 & ncol(new_columns)==0) {
+        new_columns = data.frame(id=NA)
+        colnames(new_columns)[1]=by[1]
+    }
+
     check <- all(by %in% colnames(new_columns))
     if (!check) {
         stop('parameter "by" must be a column name of the "new_columns",
             " data.frame')
     }
-
+    
     out <- struct::new_struct(
         "add_columns",
         new_columns = new_columns,
@@ -53,7 +59,7 @@ add_columns <- function(new_columns, by, ...) {
                 "annotation table. Can also be an annotation_database."
             ),
             type = c("data.frame", "annotation_database"),
-            value = data.frame(id = NA)
+            value = data.frame(value = NA)
         ),
         by = entity(
             name = "By",
@@ -71,6 +77,7 @@ add_columns <- function(new_columns, by, ...) {
 
 
 #' @export
+#' @template model_apply
 setMethod(
     f = "model_apply",
     signature = c("add_columns", "annotation_source"),

R/add_labels_class.R

@@ -69,6 +69,7 @@ add_labels <- function(labels, replace = FALSE, ...) {
 )
 
 setValidity("add_labels", method = function(object) {
+    check = FALSE
     if (length(object$labels) > 0) {
         check <- is.null(names(object$labels))
     }
@@ -81,6 +82,7 @@ setValidity("add_labels", method = function(object) {
 })
 
 #' @export
+#' @template model_apply
 setMethod(
     f = "model_apply",
     signature = c("add_labels", "annotation_source"),

R/annotation_bar_chart.R

@@ -1,4 +1,4 @@
-#' @eval get_description('annotation_pie_chart')
+#' @eval get_description('annotation_bar_chart')
 #' @include annotation_source_class.R
 #' @export
 annotation_bar_chart <- function(
@@ -103,6 +103,7 @@ annotation_bar_chart <- function(
 )
 
 #' @export
+#' @template chart_plot
 setMethod(
     f = "chart_plot",
     signature = c("annotation_bar_chart", "annotation_source"),

R/annotation_database_class.R

@@ -38,6 +38,7 @@ annotation_database <- function(
 
 
 #' @export
+#' @rdname is_writable
 setMethod(
     f = "is_writable",
     signature = c("annotation_database"),
@@ -47,6 +48,7 @@ setMethod(
 )
 
 #' @export
+#' @rdname read_source
 setMethod(
     f = "read_source",
     signature = c("annotation_database"),
@@ -58,6 +60,8 @@ setMethod(
 
 
 #' @export
+#' @rdname write_database
+#' @param df (data.frame) the data.frame to store in the database.
 setMethod(
     f = "write_database",
     signature = c("annotation_database"), definition = function(obj, df) {
@@ -76,6 +80,8 @@ setMethod(
     }
 )
 
+#' @export
+#' @rdname read_database
 setMethod(
     f = "read_database",
     signature = c("annotation_database"),

R/annotation_histogram2d_class.R

@@ -110,6 +110,7 @@ annotation_histogram2d <- function(
 
 
 #' @export
+#' @template chart_plot
 setMethod(
     f = "chart_plot",
     signature = c("annotation_histogram2d", "annotation_source"),

R/annotation_histogram_class.R

@@ -106,6 +106,7 @@ annotation_histogram <- function(
 )
 
 #' @export
+#' @template chart_plot
 setMethod(
     f = "chart_plot",
     signature = c("annotation_histogram", "annotation_source"),

R/annotation_pie_chart.R

@@ -159,6 +159,7 @@ annotation_pie_chart <- function(
 )
 
 #' @export
+#' @template chart_plot
 setMethod(
     f = "chart_plot",
     signature = c("annotation_pie_chart", "annotation_source"),

R/annotation_source_class.R

@@ -1,4 +1,4 @@
-#' @eval get_description("annotation_database")
+#' @eval get_description("annotation_source")
 #' @include zzz.R generics.R
 #' @family {annotation databases}
 #' @export
@@ -67,6 +67,7 @@ annotation_source <- function(
 
 
 #' @export
+#' @template model_apply
 setMethod(
     f = "model_apply",
     signature = c("model", "annotation_source"),
@@ -79,7 +80,7 @@ setMethod(
     }
 )
 
-#' @export
+#' @template model_apply
 setMethod(
     f = "model_apply",
     signature = c("model", "list"),
@@ -92,7 +93,7 @@ setMethod(
     }
 )
 
-#' @export
+#' @template model_apply
 setMethod(
     f = "model_apply",
     signature = c("model_seq", "list"),
@@ -105,7 +106,7 @@ setMethod(
     }
 )
 
-#' @export
+#' @template model_apply
 setMethod(
     f = "model_apply",
     signature = c("model_seq", "annotation_source"),
@@ -142,7 +143,6 @@ setMethod(
     }
 )
 
-#' @export
 setMethod(
     f = "show",
     signature = c("annotation_source"),
@@ -160,6 +160,7 @@ setMethod(
 )
 
 #' @export
+#' @rdname read_source
 setMethod(
     f = "read_source",
     signature = c("annotation_source"),
@@ -173,6 +174,7 @@ setMethod(
 )
 
 #' @export
+#' @rdname check_for_columns
 setMethod(
     f = "check_for_columns",
     signature = c("annotation_source"),
@@ -213,6 +215,18 @@ setMethod(
 
 
 #' @export
+#' @param matching_columns (list) a named list of column names that all contain 
+#' the same information. All columns named in the same list element will be 
+#' merged into a single column with the same name as the list element.
+#' @param keep_cols (character) a list of column names to keep in the final 
+#' joined table. All other columns will be dropped. 
+#' @param source_col (character) the name of a new column that will contain the 
+#' tags of the original source object for each row in the joined table.
+#' @param exclude_cols (character) the names of columns to exclude from the 
+#' joined table.
+#' @param as (character) the type of object the joined table should be returned 
+#' as e.g. "lcms_table".
+#' @rdname vertical_join
 setMethod(
     f = "vertical_join",
     signature = c("annotation_source", "annotation_source"),
@@ -278,6 +292,7 @@ setMethod(
 )
 
 #' @export
+#' @rdname vertical_join
 setMethod(
     f = "vertical_join",
     signature = c("list", "missing"),
@@ -345,7 +360,9 @@ setValidity(
     }
 )
 
+
 #' @export
+#' @rdname required_cols
 setMethod(
     f = "required_cols",
     signature = c("annotation_source"),

R/annotation_table_class.R

@@ -8,9 +8,28 @@ annotation_table <- function(
         tag = "",
         id_column = NULL,
         ...) {
+
+    # create id column if NULL    
     if (is.null(id_column)) {
-        data$.MetMashR_id <- seq_len(nrow(data))
-        id_column <- ".MetMashR_id"
+        id_column = '.MetMashR_id'
+        if (nrow(data)>0) {
+            data[[id_column]]=seq_len(nrow(data))
+        }
+    }
+
+    # create data if null
+    if (is.null(data)) {
+        data = data.frame()
+    }
+
+    # create id column if no rows or columns
+    if (nrow(data)==0 & ncol(data)==0) {
+        data <- data.frame(
+            id = character(0)
+        )
+        colnames(data) <- c(
+            id_column
+        )
     }
 
     # new object