fix spectra dep

Author: philouail

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Chromatograms
 Title: Infrastructure for Chromatographic Mass Spectrometry Data
-Version: 0.99.5
+Version: 0.99.6
 Description: The Chromatograms packages defines an efficient infrastructure
    for storing and handling of chromatographic mass spectrometry data. It
    provides different implementations of *backends* to store and represent the
@@ -30,7 +30,7 @@ Imports:
     methods,
     S4Vectors,
     MsCoreUtils (>= 1.7.5), 
-    IRanges
+    Spectra
 Suggests:
     msdata (>= 0.19.3),
     roxygen2,
@@ -39,7 +39,6 @@ Suggests:
     knitr (>= 1.1.0),
     rmarkdown,
     mzR (>= 2.41.4),
-    Spectra,
     MsBackendMetaboLights (>= 1.3.1),
     vdiffr,
     RColorBrewer

NAMESPACE

@@ -78,10 +78,10 @@ exportMethods(show)
 exportMethods(split)
 exportMethods(supportsSetBackend)
 importClassesFrom(ProtGenerics,ProcessingStep)
+importClassesFrom(Spectra,Spectra)
 importFrom(BiocParallel,SerialParam)
 importFrom(BiocParallel,bplapply)
 importFrom(BiocParallel,bpparam)
-importFrom(IRanges,NumericList)
 importFrom(MsCoreUtils,between)
 importFrom(MsCoreUtils,i2index)
 importFrom(MsCoreUtils,maxi)
@@ -90,6 +90,11 @@ importFrom(MsCoreUtils,sumi)
 importFrom(MsCoreUtils,vapply1c)
 importFrom(MsCoreUtils,vapply1l)
 importFrom(ProtGenerics,ProcessingStep)
+importFrom(Spectra,Spectra)
+importFrom(Spectra,filterRanges)
+importFrom(Spectra,peaksData)
+importFrom(Spectra,spectraData)
+importFrom(Spectra,spectraVariables)
 importFrom(grDevices,dev.flush)
 importFrom(grDevices,dev.hold)
 importFrom(grDevices,n2mfrow)

NEWS.md

@@ -1,4 +1,8 @@
-# Version 0.99.5
+# Version 0.99.6
+
+## Changes in 0.99.6
+
+- Add `Spectra` dependency.
 
 ## Changes in 0.99.5
 

R/ChromBackendSpectra.R

@@ -73,7 +73,8 @@ NULL
 #' @return Refer to the individual function description for information on the
 #'         return value.
 #'
-#' @importFrom IRanges NumericList
+#' @importClassesFrom Spectra Spectra
+#' @importFrom Spectra Spectra spectraVariables spectraData
 #'
 #' @examples
 #' library(Spectra)
@@ -130,7 +131,7 @@ ChromBackendSpectra <- setClass(
         chromData = fillCoreChromVariables(data.frame()),
         peaksData = list(.EMPTY_PEAKS_DATA),
         readonly = TRUE,
-        spectra = Spectra::Spectra(),
+        spectra = Spectra(),
         version = "0.1",
         inMemory = FALSE,
         summaryFun = sumi
@@ -141,15 +142,14 @@ ChromBackendSpectra <- setClass(
 #' @importFrom methods new
 #' @export ChromBackendSpectra
 ChromBackendSpectra <- function() {
-    .check_Spectra_package()
     new("ChromBackendSpectra")
 }
 
 #' @rdname ChromBackendSpectra
 #' @importFrom methods callNextMethod
 #' @importFrom MsCoreUtils rbindFill sumi maxi
 setMethod("backendInitialize", "ChromBackendSpectra",
-          function(object, spectra = Spectra::Spectra(),
+          function(object, spectra = Spectra(),
                    factorize.by = c("msLevel" , "dataOrigin"),
                    summarize.method = c("sum", "max"),
                    chromData = fillCoreChromVariables(),
@@ -159,7 +159,7 @@ setMethod("backendInitialize", "ChromBackendSpectra",
               if (!is(spectra, "Spectra"))
                   stop("'spectra' must be a 'Spectra' object.")
               if (!length(spectra)) return(object)
-              if (!all(factorize.by %in% Spectra::spectraVariables(spectra)))
+              if (!all(factorize.by %in% spectraVariables(spectra)))
                   stop("All 'factorize.by' variables must exist in 'spectra'.")
               if (!is.data.frame(chromData))
                   stop("'chromData' must be a 'data.frame'.")
@@ -203,14 +203,14 @@ chromSpectraIndex <- function(object) {
 setMethod("factorize", "ChromBackendSpectra",
           function(object, factorize.by = c("msLevel", "dataOrigin"),...) {
             if (!all(factorize.by %in%
-                     Spectra::spectraVariables(.spectra(object))))
+                     spectraVariables(.spectra(object))))
                   stop("All 'factorize.by' variables must be in the ",
                        "Spectra object.")
            spectra_f <- factor(
                   do.call(
                       paste,
                       c(as.list(
-                          Spectra::spectraData(.spectra(object))[,
+                          spectraData(.spectra(object))[,
                                                                factorize.by]),
                         sep = "_")))
 

R/helpers.R

@@ -208,18 +208,6 @@
     }
 }
 
-#' Used In:
-#' - `ChromBackendSpectra()`
-#' @noRd
-.check_Spectra_package <- function() {
-    if (!requireNamespace("Spectra", quietly = TRUE)) {
-        stop(
-            "The use of 'ChromBackendSpectra' requires package 'Spectra'. ",
-            "Install it using 'BiocManager::install(\"Spectra\")'"
-        )
-    }
-}
-
 #' Function to create chromData form mzml file
 #' Used In:
 #' - `backendInitialize()` for `ChromBackendMzR` class
@@ -305,14 +293,15 @@
 
 #' Used In:
 #' - `peaksData` for `ChromBackendSpectra` class.
+#' @importFrom Spectra peaksData filterRanges
 #' @noRd
 .process_peaks_data <- function(cd, s, columns, fun, drop) {
-    s <- Spectra::filterRanges(s,
+    s <- filterRanges(s,
         spectraVariables = rep("rtime", nrow(cd)),
         ranges = as.vector(rbind(cd$rtmin, cd$rtmax)),
         match = "any"
     )
-    pd <- Spectra::peaksData(s, columns = c("mz", "intensity"))
+    pd <- peaksData(s, columns = c("mz", "intensity"))
     do_rt <- "rtime" %in% columns
     do_int <- "intensity" %in% columns
     rt <- rtime(s)