fix: replace NAnnotatedDataFrame with AnnotatedDataFrame

- This fixes issue #789 by replacing the use of the deprecated and removed
  `NAnnotatedDataFrame` with the `Biobase::AnnotatedDataFrame`.

Author: jorainer

.github/workflows/check-bioc.yml

@@ -40,7 +40,7 @@ env:
   run_pkgdown: 'true'
   has_RUnit: 'false'
   has_BiocCheck: 'false'
-  cache-version: 'cache-v1'
+  cache-version: 'cache-v4'
 
 jobs:
   build-check:
@@ -100,15 +100,15 @@ jobs:
 
       - name: Cache R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: /home/runner/work/_temp/Library
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.5.3
+Version: 4.5.4
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,
@@ -49,7 +49,7 @@ Depends:
     R (>= 4.0.0),
     BiocParallel (>= 1.8.0)
 Imports:
-    MSnbase (>= 2.29.3),
+    MSnbase (>= 2.33.3),
     mzR (>= 2.25.3),
     methods,
     Biobase,

NEWS.md

@@ -1,5 +1,10 @@
 # xcms 4.5
 
+## Changes in version 4.5.4
+
+- Replace usage of deprecated (and removed) class `NAnnotatedDataFrame` with
+  `AnnotatedDataFrame`.
+
 ## Changes in version 4.5.3
 
 - Address issue #765: peak detection on chromatographic data: report a

R/XcmsExperiment-functions.R

@@ -1298,7 +1298,7 @@ XcmsExperiment <- function() {
                             processing = paste0("Data converted [", date(),"]"),
                             files = fileNames(from),
                             smoothed = NA)
-    n@phenoData <- new("NAnnotatedDataFrame", as.data.frame(sampleData(from)))
+    n@phenoData <- AnnotatedDataFrame(as.data.frame(sampleData(from)))
     fd <- as.data.frame(from@spectra@backend@spectraData)
     fnames <- unique(fd$dataStorage)
     fd$fileIdx <- match(fd$dataStorage, fnames)

R/functions-OnDiskMSnExp.R

@@ -629,8 +629,8 @@ findPeaks_MSW_Spectrum_list <- function(x, method = "MSW", param) {
     pdata <- do.call(rbind, lapply(x, pData))
     res <- new(
         "OnDiskMSnExp",
-        phenoData = new("NAnnotatedDataFrame", data = pdata),
-        featureData = new("AnnotatedDataFrame", featd),
+        phenoData = AnnotatedDataFrame(pdata),
+        featureData = AnnotatedDataFrame(featd),
         processingData = new("MSnProcess",
                              processing = paste0("Concatenated [", date(), "]"),
                              files = unlist(fls), smoothed = NA),

R/functions-XChromatograms.R

@@ -29,7 +29,7 @@
 #'     `XChromatogram` objects.
 #'
 #' @param phenoData For `XChromatograms`: either a `data.frame`,
-#'     `AnnotatedDataFrame` or `NAnnotatedDataFrame` describing the
+#'     `AnnotatedDataFrame` describing the
 #'     phenotypical information of the samples.
 #'
 #' @param featureData For `XChromatograms`: either a `data.frame` or

R/methods-XCMSnExp.R

@@ -2404,9 +2404,9 @@ setMethod("fillChromPeaks",
                       "OnDiskMSnExp",
                       processingData = new("MSnProcess",
                                            files = fileNames(object)[i]),
-                      featureData = new("AnnotatedDataFrame", fd),
-                      phenoData = new("NAnnotatedDataFrame",
-                                      data.frame(sampleNames = "1")),
+                      featureData = AnnotatedDataFrame(fd),
+                      phenoData = AnnotatedDataFrame(
+                          data.frame(sampleNames = "1")),
                       experimentData = new("MIAPE",
                                            instrumentManufacturer = "a",
                                            instrumentModel = "a",
@@ -2591,9 +2591,9 @@ setMethod("fillChromPeaks",
                       "OnDiskMSnExp",
                       processingData = new("MSnProcess",
                                            files = fileNames(object)[i]),
-                      featureData = new("AnnotatedDataFrame", fd),
-                      phenoData = new("NAnnotatedDataFrame",
-                                      data.frame(sampleNames = "1")),
+                      featureData = AnnotatedDataFrame(fd),
+                      phenoData = AnnotatedDataFrame(
+                          data.frame(sampleNames = "1")),
                       experimentData = new("MIAPE",
                                            instrumentManufacturer = "a",
                                            instrumentModel = "a",

data/faahko_sub.RData

@@ -68,7 +68,7 @@ pd <- data.frame(filename = basename(mzML_files), sample_group = grp)
 
 ## Load the data.
 ham_raw <- readMSData(files = mzML_files,
-                      pdata = new("NAnnotatedDataFrame", pd),
+                      pdata = AnnotatedDataFrame(pd),
                       mode = "onDisk")
 ```