docs: add missing links in documentation

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MsBackendMgf
 Title: Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
-Version: 1.15.1
+Version: 1.15.2
 Authors@R:
     c(person(given = "RforMassSpectrometry Package Maintainer",
              email = "[email protected]",

NEWS.md

@@ -1,5 +1,9 @@
 # MsBackendMgf 1.15
 
+## Changes in 1.15.2
+
+- Fix missing links in the documentation.
+
 ## Changes in 1.15.1
 
 - Complete unit test coverage.

R/MsBackendMgf.R

@@ -11,8 +11,8 @@ NULL
 #' from/to files in Mascot Generic Format
 #' ([mgf](http://www.matrixscience.com/help/data_file_help.html))
 #' files. After initial import, the full MS data is kept in
-#' memory. `MsBackendMgf` extends the [MsBackendDataFrame()] backend
-#' directly and supports thus the [applyProcessing()] function to make
+#' memory. `MsBackendMgf` extends the [Spectra::MsBackendDataFrame()] backend
+#' directly and supports thus the [Spectra::applyProcessing()] function to make
 #' data manipulations persistent.
 #'
 #' New objects are created with the `MsBackendMgf` function. The
@@ -63,16 +63,17 @@ NULL
 #'     be generated including the MS level, retention time and acquisition
 #'     number of the spectrum.
 #'
-#' @param x for `export`: an instance of [Spectra()] class with the data that
-#'     should be exported.
+#' @param x for `export`: an instance of [Spectra::Spectra()] class with the
+#'     data that should be exported.
 #'
 #' @param BPPARAM Parameter object defining the parallel processing
 #'     setup. If parallel processing is enabled (with `BPPARAM` different than
 #'     `SerialParam()`, the default) and length of `files` is larger than one,
 #'     import is performed in parallel on a per-file basis. If data is to be
 #'     imported from a single file (i.e., length of `files` is one), parsing
-#'     of the imported file is performed in parallel. See also [SerialParam()]
-#'     for information on available parallel processing setup options.
+#'     of the imported file is performed in parallel. See also
+#'     [BiocParallel::SerialParam()] for information on available parallel
+#'     processing setup options.
 #'
 #' @param ... Currently ignored.
 #'

R/functions-mgf.R

@@ -3,7 +3,7 @@
 ##' @description
 ##'
 ##' The `readMgf` function imports the data from a file in MGF format reading
-##' all specified fields and returning the data as a [DataFrame()].
+##' all specified fields and returning the data as a [S4Vectors::DataFrame()].
 ##'
 ##' For very large MGF files the `readMgfSplit` function might be used instead.
 ##' In contrast to the `readMgf` functions, `readMgfSplit` reads only `nlines`