refactor: import method generics from ProtGenerics

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MsBackendMassbank
 Title: Mass Spectrometry Data Backend for MassBank record Files
-Version: 1.11.1
+Version: 1.11.2
 Authors@R:
     c(person(given = "RforMassSpectrometry Package Maintainer",
              email = "[email protected]",
@@ -31,7 +31,7 @@ Imports:
     S4Vectors,
     IRanges,
     methods,
-    ProtGenerics,
+    ProtGenerics (>= 1.35.3),
     MsCoreUtils,
     DBI,
     utils
@@ -50,7 +50,7 @@ BugReports: https://github.com/RforMassSpectrometry/MsBackendMassbank/issues
 URL: https://github.com/RforMassSpectrometry/MsBackendMassbank
 biocViews: Infrastructure, MassSpectrometry, Metabolomics, DataImport
 Roxygen: list(markdown=TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Collate:
     'hidden_aliases.R'
     'MsBackendMassbank.R'

NAMESPACE

@@ -60,17 +60,17 @@ importMethodsFrom(BiocParallel,bplapply)
 importMethodsFrom(ProtGenerics,"intensity<-")
 importMethodsFrom(ProtGenerics,"mz<-")
 importMethodsFrom(ProtGenerics,"spectraNames<-")
+importMethodsFrom(ProtGenerics,backendInitialize)
 importMethodsFrom(ProtGenerics,dataStorage)
+importMethodsFrom(ProtGenerics,peaksData)
+importMethodsFrom(ProtGenerics,peaksVariables)
 importMethodsFrom(ProtGenerics,spectraNames)
 importMethodsFrom(ProtGenerics,tic)
 importMethodsFrom(Spectra,"$")
 importMethodsFrom(Spectra,"$<-")
 importMethodsFrom(Spectra,"spectraData<-")
 importMethodsFrom(Spectra,backendBpparam)
-importMethodsFrom(Spectra,backendInitialize)
 importMethodsFrom(Spectra,export)
-importMethodsFrom(Spectra,peaksData)
-importMethodsFrom(Spectra,peaksVariables)
 importMethodsFrom(Spectra,precScanNum)
 importMethodsFrom(Spectra,reset)
 importMethodsFrom(Spectra,spectraData)

NEWS.md

@@ -1,5 +1,10 @@
 # MsBackendMassbank 1.11
 
+## Changes in 1.11.2
+
+- Import method generics from `ProtGenerics`. This requires `ProtGenerics`
+  version 1.35.3.
+
 ## Changes in 1.11.1
 
 - Remove additional empty line at the end of exported MassBank records ([issue

R/MsBackendMassbank.R

@@ -95,7 +95,9 @@ setClass("MsBackendMassbank",
                                readonly = FALSE,
                                version = "0.1"))
 
-#' @importMethodsFrom Spectra backendInitialize spectraData<- $<- $
+#' @importMethodsFrom Spectra spectraData<- $<- $
+#'
+#' @importMethodsFrom ProtGenerics backendInitialize
 #'
 #' @importFrom BiocParallel bpparam
 #'

R/MsBackendMassbankSql.R

@@ -355,9 +355,7 @@ setMethod("backendInitialize", "MsBackendMassbankSql", function(object,
     object
 })
 
-#' @importMethodsFrom Spectra peaksData
-#'
-#' @importMethodsFrom Spectra peaksVariables
+#' @importMethodsFrom ProtGenerics peaksData peaksVariables
 #'
 #' @exportMethod peaksData
 #'