Squashed commit of the following:

commit c37baa7
Author: jorainer <[email protected]>
Date:   Mon Mar 18 07:59:02 2024 +0100

    fix: update required Spectra version

commit 2faed90
Author: jorainer <[email protected]>
Date:   Fri Mar 15 14:58:39 2024 +0100

    fix: require ProtGenerics 1.35.4

commit 086999d
Author: jorainer <[email protected]>
Date:   Thu Mar 14 14:46:02 2024 +0100

    refactor: cleanup NAMESPACE and dependencies and documentation

    - Re-save data object.
    - Fix documentation and unit tests following the move of `MSnbase` from Depends
      to Imports.

commit 97d7d4c
Author: jorainer <[email protected]>
Date:   Thu Mar 14 13:54:53 2024 +0100

    docs: replace inst/NEWS with NEWS.md

commit a455e6b
Author: jorainer <[email protected]>
Date:   Wed Mar 13 09:54:18 2024 +0100

    refactor: clean up namespace

    - Remove not required packages.
    - Move packages from Depends to Imports.

commit 28e4ca7
Merge: 19b1b9a 90c30b8
Author: jorainer <[email protected]>
Date:   Fri Mar 8 16:09:04 2024 +0100

    Merge branch 'devel' into jomain

commit 19b1b9a
Author: jorainer <[email protected]>
Date:   Tue Feb 27 11:04:15 2024 +0100

    refactor: ensure backward compatibility of parameter objects

commit 40c09c0
Merge: 17b487f 48ac5e0
Author: jorainer <[email protected]>
Date:   Tue Feb 27 11:01:02 2024 +0100

    Merge branch 'devel' into jomain

commit 17b487f
Merge: c36018b 1cf7cda
Author: jorainer <[email protected]>
Date:   Mon Feb 5 14:49:22 2024 +0100

    Merge branch 'devel' into jomain

commit c36018b
Author: jorainer <[email protected]>
Date:   Thu Feb 1 15:43:19 2024 +0100

    fix: call updateObject for some Param classes in as.list

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.1.10
+Version: 4.1.12
 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,
@@ -43,30 +43,26 @@ Authors@R: c(
 	   )
 Depends:
     R (>= 4.0.0),
-    BiocParallel (>= 1.8.0),
-    MSnbase (>= 2.23.1)
+    BiocParallel (>= 1.8.0)
 Imports:
+    MSnbase (>= 2.29.3),
     mzR (>= 2.25.3),
     methods,
     Biobase,
     BiocGenerics,
-    ProtGenerics (>= 1.35.2),
+    ProtGenerics (>= 1.35.4),
     lattice,
-    RColorBrewer,
-    plyr,
-    RANN,
     MassSpecWavelet (>= 1.66.0),
     S4Vectors,
-    robustbase,
     IRanges,
     SummarizedExperiment,
     MsCoreUtils (>= 1.15.3),
     MsFeatures,
     MsExperiment (>= 1.5.4),
-    Spectra (>= 1.13.2),
+    Spectra (>= 1.13.7),
     progress,
-    multtest,
     jsonlite,
+    RColorBrewer,
     MetaboCoreUtils (>= 1.11.2)
 Suggests:
     BiocStyle,
@@ -80,19 +76,21 @@ Suggests:
     rmarkdown,
     MALDIquant,
     pheatmap,
+    RANN,
+    multtest,
     MsBackendMgf,
     signal,
     mgcv
 Enhances:
     Rgraphviz,
-    rgl,
-    XML
+    rgl
 License: GPL (>= 2) + file LICENSE
 URL: https://github.com/sneumann/xcms
 BugReports: https://github.com/sneumann/xcms/issues/new
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, MassSpectrometry, Metabolomics
 RoxygenNote: 7.3.1
+Encoding: UTF-8
 Collate:
     'AllGenerics.R'
     'functions-XChromatograms.R'

NAMESPACE

@@ -1,11 +1,10 @@
-useDynLib(xcms)
+useDynLib(xcms, .registration = TRUE)
 
-importFrom("utils", "capture.output", "data")
 import("methods")
 importMethodsFrom("ProtGenerics", "peaks", "chromatogram", "writeMSData",
     "polarity<-", "centroided", "isCentroided", "peaks<-",
     "isolationWindowTargetMz", "quantify", "bin", "spectrapply",
-    "filterFeatures", "filterMzRange")
+    "filterFeatures", "filterMzRange", "filterRt", "filterMz", "filterMsLevel")
 importClassesFrom("ProtGenerics", "Param")
 importFrom("BiocGenerics", "updateObject", "fileName", "subset",
     "dirname", "dirname<-")
@@ -18,18 +17,12 @@ importMethodsFrom("Biobase", "phenoData",
 importFrom("IRanges", "CharacterList", "NumericList")
 importClassesFrom("IRanges", "CharacterList", "NumericList")
 
-importFrom("graphics", "image", "boxplot", "matplot", "rect", "axis",
-           "grid", "mtext", "polygon", "box", "plot.xy")
 importFrom("mzR", "peaks", "close", "openMSfile", "header")
 importFrom("lattice", "levelplot", "panel.rect", "panel.levelplot",
            "level.colors", "do.breaks")
-importFrom("plyr", "rbind.fill")
-importFrom("robustbase", "lmrob", "lmrob.control")
-import("RColorBrewer")
-import("BiocParallel")
-## importMethodsFrom("stats4", "plot")
+importFrom("BiocParallel", "bpparam", "SerialParam")
+importMethodsFrom("BiocParallel", "bplapply", "bpmapply")
 
-## import("S4Vectors")
 importClassesFrom("S4Vectors", "Rle", "DataFrame", "Hits")
 importFrom("S4Vectors", "split", "Rle", "DataFrame", "SimpleList", "List",
            "as.matrix")
@@ -41,12 +34,13 @@ importFrom("SummarizedExperiment", "rowData<-")
 importFrom("SummarizedExperiment", "assay")
 importFrom("MsCoreUtils", "rbindFill", "closest", "i2index", "sumi", "between",
            "maxi", "breaks_ppm")
+importFrom("RColorBrewer", "brewer.pal")
 
-## Additional imports proposed by R CMD check:
-importFrom("graphics", "abline", "barplot", "close.screen", "hist",
-           "identify", "layout", "legend", "lines", "par", "plot.new",
-           "plot.window", "points", "screen", "split.screen",
-           "strwidth", "text", "title")
+importFrom("graphics", "image", "boxplot", "matplot", "rect", "axis",
+           "grid", "mtext", "polygon", "box", "plot.xy", "abline",
+           "barplot", "close.screen", "hist", "identify", "layout",
+           "legend", "lines", "par", "plot.new", "plot.window", "points",
+           "screen", "split.screen", "strwidth", "text", "title")
 importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.cur",
            "dev.list", "dev.off", "dev.set", "palette", "pdf", "png",
            "rainbow", "rgb", "terrain.colors", "n2mfrow", "dev.flush",
@@ -58,11 +52,8 @@ importFrom("stats", "aov", "approx", "convolve", "cor", "deriv3",
            "rnorm", "runif", "dbeta", "resid")
 importFrom("utils", "flush.console", "head", "object.size",
            "packageVersion", "read.csv", "tail", "write.csv",
-           "write.table")
+           "write.table", "capture.output", "data")
 
-## New imports from packages moved from Suggests to Imports:
-importFrom("multtest", "mt.teststat")
-importFrom("RANN", "nn2")
 importFrom("MassSpecWavelet", "peakDetectionCWT", "tuneInPeakInfo")
 
 ## MSnbase:
@@ -595,6 +586,8 @@ importFrom("progress", "progress_bar")
 exportClasses("XcmsExperiment")
 exportMethods("uniqueMsLevels")
 exportMethods("filterMzRange")
+exportMethods("fromFile")
+exportMethods("fileNames")
 
 ## saving xcms objects things
 importFrom("jsonlite", "serializeJSON", "write_json", "unserializeJSON",