the relevant documentation examples now use the in-package example da…

…ta file

R/binneRlyse.R

@@ -18,6 +18,7 @@
 #' @seealso \code{\link{Binalysis-class}}, \code{\link{binParameters}}, 
 #' \code{\link{sampleInfo}}, \code{\link{binnedData}},  \code{\link{accurateData}}
 #' @examples 
+#' \dontrun{
 #' files <- metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')
 #' 
 #' info <- metaboData::runinfo('FIE-HRMS','BdistachyonTechnical')
@@ -31,6 +32,7 @@
 #' analysis <- binneRlyse(files, 
 #'                        info, 
 #'                        parameters = parameters)
+#' }
 #' @importFrom dplyr ungroup n
 #' @importFrom magrittr %>%
 #' @importFrom crayon blue red green

R/detect.R

@@ -6,12 +6,9 @@
 #' @return Numeric vector of detected infusion scans.
 #' @seealso \code{\link{detectParameters}}
 #' @examples 
-#' if (requireNamespace("metaboData", quietly = TRUE)) {
-#'    detectInfusionScans(
-#'       metaboData::filePaths('FIE-HRMS',
-#'                             'BdistachyonTechnical',
-#'                             ask = FALSE)[1])
-#' }
+#' file_paths <- system.file('example-data/1.mzML.gz',package = 'binneR')
+#' 
+#' detectInfusionScans(file_paths)
 #' @importFrom mzR openMSfile header
 #' @importFrom dplyr group_by summarise
 #' @export
@@ -71,8 +68,8 @@ detectInfusionScans <- function(files,
 #' @param files character vector of file paths
 #' @return S4 object of class BinParameters
 #' @examples 
-#' files <- metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')
-#' parameters <- detectParameters(files[1])
+#' file_paths <-system.file('example-data/1.mzML.gz',package = 'binneR')
+#' parameters <- detectParameters(file_paths)
 #' @seealso \code{\link{BinParameters-class}}, \code{\link{binParameters}}
 #' @export
 

R/plot.R

@@ -138,8 +138,10 @@ setMethod('plotChromatogram',signature = 'Binalysis',
 #' @param files character vector of file paths to use
 #' @param scans specify scans to highlight within the plot
 #' @examples 
-#' plotChromFromFile(metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')[1],
-#'                             scans = c(6,18))
+#' file_paths <- system.file('example-data/1.mzML.gz',package = 'binneR')
+#' 
+#' plotChromFromFile(file_paths, 
+#'                   scans = detectInfusionScans(file_paths))
 #' @export
 
 plotChromFromFile <- function(files, scans = c()){

R/readFiles.R

@@ -13,16 +13,15 @@
 #' and \code{?future::plan} for details on how this can be specified.
 #' @examples 
 #' ## Example file path
-#' file_paths <- metaboData::filePaths('FIE-HRMS',
-#'                                     'BdistachyonTechnical')[1]
+#' file_paths <- system.file('example-data/1.mzML.gz',package = 'binneR')
 #' 
 #' ## Optionally declare parallel processing backend
 #' # plan(future::multisession,workers = 2)
 #'                                                                         
 #' ## Process example file
 #' res <- readFiles(file_paths,
 #'                  dp = 2,
-#'                  scans = 6:17)
+#'                  scans = detectInfusionScans(file_paths))
 #'
 #' @importFrom furrr future_map
 #' @importFrom dplyr bind_rows 

R/singleSample.R

@@ -15,12 +15,14 @@
 #' \code{binner_dp} or the environment variable \code{BINNER_DP}.
 #' 
 #' @examples 
+#' \dontrun{
 #' file_path <- metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')[1]
 #' 
 #' ## Optionally declare parallel processing backend
 #' # plan(future::multisession,workers = 2)
 #' 
 #' bd <- singleSample(file_path)
+#' }
 #' @importFrom utils capture.output
 #' @export