diff --git a/DESCRIPTION b/DESCRIPTION
index 16b9837f8..642c59c1e 100644
--- a/DESCRIPTION
+++ b/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'
diff --git a/NAMESPACE b/NAMESPACE
index b59faa1a4..bd9806399 100644
--- a/NAMESPACE
+++ b/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",
diff --git a/NEWS.md b/NEWS.md
new file mode 100644
index 000000000..6578300b6
--- /dev/null
+++ b/NEWS.md
@@ -0,0 +1,1263 @@
+# xcms 4.1
+
+## Changes in version 4.1.11
+
+- Clean up of required and suggested packages and namespace imports.
+- Re-creation of bundled data objects.
+
+## Changes in version 4.1.10
+
+- Ensure backward compatibility for parameter objects that gained additional
+  slots.
+
+## Changes in version 4.1.9
+
+- Fix bug in `filterFeatures,PercentMissingFilter`.
+
+## Changes in version 4.1.8
+
+- Fixing issue #716: edit of `.empty_chrom_peaks` function so an `sn` column is
+  returned. Fixes extracting and plotting of peaks after using
+  `manualChromPeaks`
+
+## Changes in version 4.1.7
+
+- Implementation of `filterFeatures` function with `filter` parameters:
+  `RsdFilter`, `DratioFilter`, `PercentMissingFilter`, `BlankFlag`. They can be
+  used ot filter features from `XcmsResult` and `SummarizedExperiment` objects.
+- Addition of a section in the main xcms vignette to describe how to use it.
+
+## Changes in version 4.1.6
+
+- Import `filterSpectra` from `MsExperiment`.
+- Import `breaks_ppm` from `MsCoreUtils`.
+- Update `featureArea` function to consider all chromatographic peaks per
+  feature, not only the one with the highest intensity. As a consequence,
+  returned m/z and rt ranges might be higher which has an influence in
+  `featureChromatograms`, EIC-based feature grouping and, to a lesser extent
+  also in gap-filling. Related documentation was updated.
+- Improve performance of the `featureArea` function (and related of the
+  `PeakAreaParam`-based gap filling).
+- Add parameter `ppm` to `PeakDensityParam` to enable peak-density-based
+  correspondence throgh m/z-dependent bins along the m/z.
+
+## Changes in version 4.1.5
+
+- Improve performance of the `chromatogram` call for `XcmsExperiment` objects.
+- Remove internal (not exported) normalization functions. These have been
+  transferred to the MetaboCoreUtils package.
+- Support subsetting of `XcmsExperiment` with negative indices.
+
+## Changes in version 4.1.4
+
+- Rename variable `data` in the vignette to `faahko`.
+- Fix issue in adjustRtime resulting in corrupt processHistory.
+- Add support to perform peakGroups alignment using pre-defined anchor peak
+  matrix (i.e., the numeric matrix with retention times of anchor peaks in
+  the samples that can be used to align these samples).
+- Fix errors related to invalid `Chromatogram` objects extracted from xcms
+  results: ensure MS level in `chromPeaksMatrix` is `integer`.
+- Fix definition of anchor peaks for peakGroups alignment with subset
+  (issue #702).
+- Add `filterMsLevel` method for `MsExperiment` and `XcmsExperiment`.
+- Ensure chunk-wise processing of Spectra (introduced with version 1.13.2) is
+  disabled when xcms is using its own chunk-wise processing.
+
+## Changes in version 4.1.3
+
+- Add parameter `verboseBetaColumns` to `CentWaveParam` to enable calculation
+  of additional peak quality metrics comparing the EIC to an idealized bell
+  curve.
+
+## Changes in version 4.1.2
+
+- Add a `param =` to generic function `storeResults`: `PlainTextParam` to save
+  an `XcmsExperiment` or `MsExperiment` object as colleciton of plain text
+  files.
+
+## Changes in version 4.1.1
+
+- Add method `storeResults` and one of its `param =`: `RDataParam` to save an
+  `XcmsExperiment` object as an .RData file.
+
+
+# xcms 3.99
+
+## Changes in version 3.99.6
+
+- Add method to coerce a `XcmsExperiment` to a `xcmsSet` (issue #696).
+- Support providing only `mz` or `rt` also for `chromatogram,MsExperiment`.
+
+## Changes in version 3.99.5
+
+- Only `mz` or `rt` need to be provided for `chromatogram`.
+
+## Changes in version 3.99.4
+
+- Add `chromPeakChromatograms` function to extract (EIC) chromatograms for
+  chromatographic peaks.
+
+## Changes in version 3.99.3
+
+- Small fixes in the *direct injection* vignette.
+- Add parameter `isolationWindowTargetMz` to the `chromatogram` function for
+  `MsExperiment` and `XcmsExperiment` to ensure MS2 chromatographic data is
+  extracted from the MS2 spectra containing fragments of the compound of
+  interest.
+
+## Changes in version 3.99.2
+
+- Add the `xmse` data set representing an `XcmsExperiment` object.
+- Update the *compounding* vignette to use the new objects.
+- Add `loadXcmsData` to load test data objects (and fix/update paths).
+- Add `groupFeatures` methods for `XcmsExperiment`.
+- Fix issue in `featureArea` for `XcmsExperiment`.
+- Update main vignette to use and describe the new data objects.
+- Add `findChromPeaksIsolationWindow` method for `MsExperiment` and
+  `XcmsExperiment`.
+- Make `reconstructChromPeakSpectra` a method.
+- Add `reconstructChromPeakSpectra` implementation for `XcmsExperiment`.
+- Add `filterIsolationWindow` for `MsExperiment` and `XcmsExperiment` to filter
+  spectra (and eventually chromatographic peaks) based on the isolation window.
+- Update the LC-MS/MS vignette adding also an example how to deisotope SWATH
+  MS2 spectra.
+
+## Changes in version 3.99.1
+
+- `featureSummary` and `overlappingFeatures` gain support for `XcmsExperiment`.
+- Fix in `featureChromatograms` to ensure a valid object is returned.
+
+## Changes in version 3.99.0
+
+- Add `XcmsExperiment` and support for `MsExperiment`/`Spectra`: add all
+  functionality for a full xcms processing on a `MsExperiment` object.
+- Fix issue in `refineChromPeaks` with `MergeNeighboringPeaksParam` where a
+  wrong apex position was considered in the evaluation whether candidate peaks
+  should be merged (would only happen for merging of > 2 candidate peaks).
+- Re-write the `reconstructChromPeakSpectra` for DIA data analysis to fix an
+  issue with chromatographic peaks in overlapping SWATH isolation windows and
+  generally to improve performance.
+
+
+# xcms 3.21
+
+## Changes in version 3.21.5
+
+- Fix issue in `chromatogram` after filtering a result object (issue #511).
+
+## Changes in version 3.21.4
+
+- Move multtest from Suggests to Imports in dependencies
+
+## Changes in version 3.21.3
+
+- Only fixes in the long running tests
+
+## Changes in version 3.21.1
+
+- Fix error with `fillChromPeaks` on sparse data (many empty spectra) and peak
+  detection performed with `MatchedFilterParam` (issue #653).
+- Update to newer function names in the `rgl` package (issue #654).
+
+
+# xcms 3.19
+
+## Changes in version 3.19.2
+
+- Update/expand documentation for the `firstBaselineCheck` parameter of
+  centWave.
+
+## Changes in version 3.19.1
+
+- Update documentation to reference updates in MassSpecWavelet package.
+
+
+# xcms 3.17
+
+## Changes in version 3.17.6
+
+- Rewrite code to subset features and chromatographic peaks. This results in a
+  perfomance improvement for `filterFile` and similar functions.
+- Add parameter `expandMz` to `featureChromatograms`
+  https://github.com/sneumann/xcms/issues/612.
+
+## Changes in version 3.17.5
+
+- Change the way the m/z value for a chromatographic peak is determined by
+  centWave: if a ROI contains more than one peak for one scan (spectrum) an
+  intensity-weighted m/z is reported for that scan. The m/z of the
+  chromatographic peak is then calculated based on these reported m/z values for
+  each scan (spectrum). In the original version the mean m/z for a scan was
+  reported instead. As a result, m/z values of chromatographic peaks are now
+  slightly different but are expected to be more accurate. See
+  https://github.com/sneumann/xcms/issues/590 for more details.
+
+## Changes in version 3.17.4
+
+- Add `transformIntensity` method.
+- Fix issue when calling `chromPeakSpectra` or `featureSpectra` on an object
+  that contains also files with only MS1 spectra
+  (https://github.com/sneumann/xcms/issues/603).
+
+## Changes in version 3.17.2
+
+- Use mzML instead of mzData files in testing and vignettes,
+  since mzR drop mzData reading and msdata package will drop mzData files as well
+
+## Changes in version 3.17.1
+
+- Fix bug in feature grouping by EIC correlation that would return a
+  non-symmetric similarity matrix.
+- Fix error message from issue [584](https://github.com/sneumann/xcms/issues/584).
+
+
+# xcms 3.15
+
+## Changes in version 3.15.5
+
+- Disable testing on windows i386, providing some speedup
+- Disable parallel processing on Windows, causing an issue in testthat on BioC build check
+
+## Changes in version 3.15.4
+
+- Fix in `plot` with `type = "XIC"` to plot an empty plot if no data is present.
+- Skip re-indexing of peaks to features if not necessary. This results in
+  performance improvements for MS1 only data.
+
+## Changes in version 3.15.3
+
+- Add `manualFeatures` allowing to manually define and add features to an
+  `XCMSnExp` object.
+- Add `plotChromatogramsOverlay` function to support plotting of multiple EICs
+  from the same sample into the same plot (eventually stacked).
+- Add feature grouping by EIC similarity: `EicSimilarityParam`.
+- Import `compareChromatograms` from `MSnbase`.
+- Add feature grouping by similar retention time: `SimilarRtimeParams.
+- Add feature grouping by similarity of feature abundances across samples:
+  `AbundanceSimilarityParam`.
+- Add feature grouping methodology based on `MsFeatures`.
+
+## Changes in version 3.15.2
+
+- Fix LC-MS/MS vignette.
+
+## Changes in version 3.15.1
+
+- Compatibility fix for nls() in R >= 4.1, contributed by Rick Helmus.
+
+
+# xcms 3.13
+
+## Changes in version 3.13.8
+
+- Fix plotQC() for XCMSnExp objects
+
+## Changes in version 3.13.7
+
+- Add `featureArea` function to extract the m/z-rt region for features.
+- Fix `featureSpectra` function.
+- Re-add the LC-MS/MS vignette.
+- Feature: plotQC() supports XCMSnExp objects now
+
+## Changes in version 3.13.6
+
+- Fix issue #545: skip second centWave run with CentWavePredIsoParam in regions
+  of interest with undefined peak boundaries/scan ranges.
+- Temporarily remove the LC-MS/MS vignette (until MsBackendMgf is added to
+  Bioconductor).
+
+## Changes in version 3.13.5
+
+- Add `filterChromPeaks` method to filter chromatographic peaks in a
+  `XChromatogram` or `XChromatograms` object.
+- Add `filterChromPeaks` method for `XCMSnExp` (issue #541).
+- Support return of `Spectra` objects by `chromPeakSpectra`, `featureSpectra`
+  and `reconstructChromPeakSpectra`.
+- Support extraction of MS1 spectra with `chromPeakSpectra`.
+- Support extraction of the spectrum with the largest total signal or largest
+  base peak signal in `chromPeakSpectra`.
+- Add support for extraction of spectra for selected/individual peaks/features
+  using the `peaks` and `features` parameter in `chromPeakSpectra` and
+  `featureSpectra`, respectively.
+
+## Changes in version 3.13.4
+
+- Import `Param` object from `ProtGenerics`.
+- Import `filterIntensity`, `normalize` and `alignRt` for `Chromatogram` and
+  `MChromatograms` from `MSnbase`.
+
+## Changes in version 3.13.3
+
+- `align,Chromatogram` gains new method `"none"` which will only keep values
+  with identical retention times. For `method = "matchRtime"` the (much faster)
+  matching function `closest` from the `MsCoreUtils` package is used.
+- Method `correlate,Chromatogram` gains parameter `useIntensitiesAbove` to
+  perform the correlation only with values larger than this threshold
+  (avoiding thus high correlation because of many 0-values).
+- Add method `filterIntensity,Chromatogram` that allows to filter a chromatogram
+  object keeping only data points with an intensity above a user provided
+  threshold.
+
+## Changes in version 3.13.2
+
+- Add new function `manualChromPeaks` allowing to manually add and integrate
+  chromatographic peaks.
+
+## Changes in version 3.13.1
+
+- Support subsetting of `XChromatograms` with `drop = FALSE`.
+
+
+# xcms 3.11
+
+## Changes in version 3.11.8
+
+- Disable parallel processing in vignettes.
+
+## Changes in version 3.11.7
+
+- More efficient splitting data per file especially for larger data sets.
+- Disable parallel processing in examples.
+
+## Changes in version 3.11.6
+
+- Add `FilterIntensityParam` to filter chromatographic peaks on intensity
+  (issue #502).
+- Add `estimatePrecursorIntensity` function to determine the precursor intensity
+  for MS2 spectra from the neighboring MS1 spectra.
+
+## Changes in version 3.11.4
+
+- Change from `Spectra` and `Chromatograms` to `MSpectra` and `MChromatograms`
+  from MSnbase version >= 2.15.3.
+
+## Changes in version 3.11.3
+
+- `reconstructChromPeakSpectra`: report also polarity and `precusorIntensity`.
+- `reconstructChromPeakSpectra`: ensure a retention time is reported for
+  reconstructed MS2 spectra (issue #485).
+- Change default for `expandRt` to `0` in `reconstructChromPeakSpectra`.
+- Fix error in `refineChromPeaks,MergeNeighboringPeaksParam` if no peaks found
+  to be merged.
+
+## Changes in version 3.11.2
+
+- Add `fillChromPeaks,ChromPeakAreaParam` to base the area from which missing
+  peak data should be filled-in on the actually detected chromatographic peaks
+  of a feature.
+- Potential fix for issue #481: function should no longer throw an error because
+  retention times are of length 0.
+- More efficient splitting of processing which should increase the speed of
+  the findChromPeaks, refineChromPeaks, reconstructChromPeakSpectra and
+  chromPeakSpectra calls.
+
+## Changes in version 3.11.1
+
+- Fix issue #471: conversion from `XCMSnExp` to `xcmsSet` looses phenodata
+  (thanks to Andris Jankevics for reporting and providing a solution).
+- Add `normalize` method for `Chromatogram` and `Chromatograms` objects.
+- `featureChromatograms` gets new parameter `n` and `value` to extract EICs
+  only from the top n samples with highest intensities.
+- `filterFile` gets new parameter `keepFeatures` to support retaining
+  correspondence results even if a data set is filtered by file.
+- Export the virtual `Param` class.
+- Add filterColumnsIntensityAbove method for Chromatograms object that allows
+  to select columns (samples) of an Chromatograms object for which intensities
+  of its chromatographic data are higher than a threshold.
+- Add removeIntensity method for Chromatogram, Chromatograms, XChromatogram
+  and XChromatograms objects allowing to *remove* intensities based on different
+  criteria.
+- Add correlate method for Chromatograms allowing to correlate multiple
+  chromatograms with each other.
+
+
+# xcms 3.9
+
+## Changes in version 3.9.4
+
+- Fix issue in centWave which skips peak detection depending on minimum
+  peakwidth (issue #445): add parameter `extendLengthMSW` in `CentWaveParam`.
+  Thanks to William Kumler for contributing the fix.
+- Tentatively reduce memory requirements in `fillChromPeaks`.
+- Fix issue #467 for fillPeaks() of an xcmsSet converted from an XCMSnSet
+
+## Changes in version 3.9.3
+
+- Move multtest from Imports to Suggests to avoid duplicated method definition
+  for plot (issue #459).
+- Add support for peak filling from MS level > 1 to fillChromPeaks.
+- featureValues gains parameter msLevel to extract feature values for features
+  of all, or from a specific MS level.
+- refineChromPeaks supports different MS levels.
+- Added support to perform correspondence analysis on MS level > 1 and add the
+  respective results to already present feature definitions.
+- hasChromPeaks and hasFeatures gain parameter msLevel to check for presence of
+  chromatographic peaks or features from a specific MS level.
+
+## Changes in version 3.9.2
+
+- Fix featureChromatograms and chromatograms on a XCMSnExp object with features:
+  features can be duplicated across rows (EICs).
+- findChromPeaks: add parameter `add` to allow several rounds of peak detections
+  on the same object.
+- Small performance enhancement in fillChromPeaks.
+- Better support for MS > 1 data in fillChromPeaks: skip MS level 2 spectra for
+  filling in.
+- Add refineChromPeaks for XChromatogram and XChromatograms objects.
+- Add groupOverlaps function to group arbitrary ranges.
+- Add quantify,XCMSnExp object to quantify an XCMSnExp into a
+  SummarizedExperiment.
+- Fine-tune MergeNeighboringPeaks peak refinement method: the average of the
+  3 data points between candidate peaks is used to evaluate whether the peaks
+  should be merged making the approach more robust against outliers. In
+  addition, an ion chromatogram for candidate peaks is extracted with an m/z
+  range expanded depending on the expandMz and ppm setting ensuring that low
+  intensity data points between candidate peaks are not missed out (because
+  their m/z might be slightly shifted on ToF instruments). The mzmin and mzmax
+  of the merged peak represents also the minimum and maximum m/z of all data
+  points in that extracted ion chromatogram.
+
+## Changes in version 3.9.1
+
+- Fix problem of not shown/plotted peak positions in plotChromPeakSpectra
+  for experiments in which peaks were not detected in the first sample(s).
+- Add method *from_to* to missing value imputation method `imputeRowMinRand`.
+- Show warning in findChromPeaks if empty spectra are detected.
+- Add refineChromPeaks method and CleanPeaksParam class to allow removal of
+  chromatographic peaks exceeding a user-definable maximal peak width.
+- Add MergeNeighboringPeaksParam for refineChromPeaks to allow merging of
+  chromatographic peaks close in m/z and retention time with a signal between
+  them higher than a certain threshold (issue #414).
+- Fix misspelled parameter `mzd` in LC-MS/MS vignette.
+
+
+# xcms 3.7
+
+## Changes in version 3.7.5
+
+- Remove xcmsMSn vignette (based on old xcms).
+
+## Changes in version 3.7.4
+
+- mzClust correspondence analysis: check and fix missing values in column mz of
+  the peaks matrix (issue #416).
+
+## Changes in version 3.7.3
+
+- plot type = "XIC" on an XCMSnExp object will draw rectangles indicating the
+  identified chromatographic peaks.
+- Add a vignette describing LC-MS/MS data analysis with xcms.
+
+## Changes in version 3.7.2
+
+- Fix documentation (issue #401).
+- Add support for SWATH data analysis.
+
+## Changes in version 3.7.1
+
+- Add correlate method for Chromatogram objects.
+- Add parameter lwd to plotAdjustedRtime.
+- Add align method for Chromatogram objects.
+- Add findChromPeaksIsolationWindow to enable chromatographic peak detection
+  in isolation windows.
+- Fix issue in chromPeakSpectra with method = "signal".
+- chromPeakSpectra and featureSpectra return now MS2 spectra with an precursor
+  m/z >= mzmin, <= mzmax and retention time >= rtmin, <= rtmax.
+- Improve performance of chromPeakSpectra and featureSpectra.
+
+
+# xcms 3.5
+
+## Changes in version 3.5.5
+
+- Add dirname and dirname<- methods for OnDiskMSnExp to change the path to the
+  raw data files.
+- Add section "Subset-based alignment" to the xcms vignette to describe the
+  alignment possibility to perform alignments based on a subset of samples
+  (e.g. QC samples).
+
+## Changes in version 3.5.4
+
+- Fix problem in featureChromatograms with include = "feature_only" that could
+  return a non-valid object.
+- Ensure that XCMSnExp objects are updated if necessary in all analysis methods.
+
+## Changes in version 3.5.3
+
+- Fix unit tests.
+
+## Changes in version 3.5.2
+
+- Small changes in fillChromPeaks,XCMSnExp to reduce memory demand.
+- Fix issue #359.
+- Fix issue #360: rawEIC skipped last scan/spectrum if rtrange was provided.
+- filterMsLevel keeps now chromatographic peaks and feature definitions from the
+  specified MS levels (issue #362).
+- Fix bug in `xcmsRaw` that leads to a netCDF error message (issue #363).
+- Add parameter msLevel to chromPeaks for XCMSnExp objects.
+- Add chromPeakData to allow adding arbitrary annotation to chromatographic
+  peaks.
+- Change default of parameter value in featureValues from value = "index" to
+  value = "into".
+- Add parameter isFilledColumn to chromPeaks allowing the old behaviour to
+  include the is_filled column in the chromatographic peak matrix.
+
+## Changes in version 3.5.1
+
+- Fix issue #349.
+- Add updateObject function for XCMSnExp objects (issue #347).
+- Add dropFilledChromPeaks methods for XChromatogram and XChromatograms objects.
+- Add parameter filled = FALSE to chromatogram and featureChromatograms
+  functions.
+- Fix matchedFilter peak detection problems with empty spectra (issue #325).
+- featureChromatograms extracts by default only chromatographic peaks associated
+  with a feature.
+- chromatogram,XCMSnExp extracts an XChromatogram containing also
+  chromatographic peaks and feature definitions.
+- Add featureValues method for XChromatograms objects (issue #336).
+- Add correspondence analysis (peak grouping) for chromatographic data (for now
+  only with PeakDensity method; issue #336).
+- Add featureDefinitions slot to XChromatograms object and related accessor
+  methods.
+- Add subset alignment option subsetAdjust = "average" to adjust left-out
+  samples (blanks or simply non-subset samples) based on an interpolation from
+  the results of the previous and subsequent subset sample.
+- Add parameter subsetAdjust to PeakGroupsParam allowing to switch between
+  different methods to adjust samples left out in the alignment process.
+- Alignment based on a sample subset for the peak groups method (issue #335):
+  sample subset can be defined with the subset parameter, samples not included
+  in the subset will be aligned based on the adjusted retention times of the
+  closest sample in the subset.
+- Add findChromPeaks,XChromatograms (issue #332).
+- Add processHistory,XChromatograms.
+- Add plot,XChromatograms method with automatic peak highlighting (issue #334).
+- Add hasChromPeaks,XChromatograms method.
+- Add XChromatograms class with constructor function and coercing method.
+- Add hasChromPeaks,XChromatogram method.
+- Add filterRt,XChromatogram, filterMz,XChromatogram.
+- Add plot,XChromatogram function supporting of highlighting/drawing identified
+  chromatographic peaks.
+- findChromPeaks,Chromatogram returns an XChromatogram object (issue #329).
+- Add chromPeaks,XChromatogram (issue #329).
+- Add XChromatogram object (issue #329).
+- Fix higlightChromPeaks with type = "polygon": peak filling represents now the
+  full detected peak and is no longer cut by the provided rt.
+- Add argument peakIds to highlightChromPeaks allowing to specify the IDs of
+  peaks to be highlighted.
+- Add example on clustering of base peak chromatograms to the vignette (issue
+  #328).
+- Small fix in the vignette (issue #327).
+- Add parameter groupval to exportMetaboAnalyst (issue #296).
+- Fix bug in show,XCMSnExp that would throw an error if no process history is
+  present.
+
+
+# xcms 3.3
+
+## Changes in version 3.3.6
+
+- Add type = "polygon" to highlightChromPeaks allowing to fill the actual
+  signal area of identified chromatographic peaks.
+
+## Changes in version 3.3.5
+
+- Performance enhancement of the chromPeakSpectra and featureSpectra functions.
+
+## Changes in version 3.3.4
+
+- Add featureChromatograms to extract ion chromatograms for each feature.
+- Add hasFilledChromPeaks function.
+- Add argument skipFilled to the featureSummary function.
+
+## Changes in version 3.3.3
+
+- Add chromPeakSpectra and featureSpectra functions to extract MS2 spectra
+  for chromatographic peaks and features, respectively (issue #321).
+- Fix profMat to handle also data files with empty spectra (issue #312).
+- Add argument ylim to plotAdjustedRtime (issue #314).
+- Add imputeRowMin and imputeRowMinRand, two simple missing value imputation
+  helper functions.
+- Fix additional problem mentioned in issue #301 with obiwarp retention time
+  correction if some spectra have m/z values of `NA`.
+- Fix issue #300 avoiding chromatographic peaks with rtmin > rtmax.
+- Fixes for issues #291, #296.
+- Add parameter 'missing' to diffreport allowing to replace NA with arbitrary
+  numbers.
+- Add exportMetaboAnalyst function to export the feature matrix in MetaboAnalyst
+  format.
+- Add parameter missing to featureValues allowing to specify how to handle/
+  report missing values.
+- The chromPeaks matrix has now rownames to uniquely identify chromatographic
+  peaks in an experiment. Chromatographic peak IDs start with "CP" followed by
+  a number.
+
+## Changes in version 3.3.2
+
+- Add writeMSData method for XCMSnExp allowing to write mzML/mzXML files with
+  adjusted retention times (issue #294).
+- Fix profEIC call for single-scan-peak (pull request #287 from @trljcl).
+- Fix centWave avoiding that the same peak is reported multiple times if
+  fitgauss = TRUE is used (issue #284).
+- featureSummary reports also RSD (relative standard deviations) of features
+  across samples (issue #286).
+- Add parameters fixedMz and fixedRt to FillChromPeaksParam that allow to
+  increase the features' m/z and rt widths by a constant factor.
+- Add option "sum" to featureValues' method parameter allowing to sum the
+  intensities of peaks that are assigned to the same feature in a file/sample.
+
+## Changes in version 3.3.1
+
+- Add overlappingFeatures function to identify overlapping or close features.
+- Add support for type = "apex_within" for featureDefinitions.
+- Fix a bug in fillChromPeaks that would return the integrated signal being Inf.
+- Fix for issue #267: error in fillChromPeaks when the retention time of the
+  peaks are outside of the retention time range of certain files.
+- New featureSummary function to calculate basic feature summaries (number of
+  samples in which peaks were found etc).
+- Parameter 'type' added to plotChromPeakDensity and 'whichPeaks' to
+  highlightChromPeaks. Both parameters are passed to the 'type' argument
+  of chromPeaks.
+- Parameter 'type' in chromPeaks gets additional option "apex_within" to return
+  chromatographic peaks that have their apex within the defined rt and/or m/z
+  range.
+- Add functions rla and rowRla to calculate RLA (relative log abundances).
+- Add peaksWithMatchedFilter to perform peak detection in chromatographic
+  (MRM/SRM) data (issues #277 and #278).
+- Add peaksWithCentWave to perform centWave peak detection in chromatographic
+  (MRM/SRM) data (issue #279).
+- Add findChromPeaks,Chromatogram methods for CentWaveParam and
+  MatchedFilterParam (issue #280).
+
+
+# xcms 3.1
+
+## Changes in version 3.1.3
+
+- Fix misplaced parenthesis in the check for multiple spectra in
+  findChromPeaks,OnDiskMSnExp,MSWParam. Thanks to @RonanDaly (PR #276).
+- Update link to correct metlin page in diffreport result (issue #204).
+
+## Changes in version 3.1.2
+
+- Add filterFeatureDefinitions function.
+- Fix #273: better error message in case not a single feature could be defined
+  by groupChromPeaks.
+
+## Changes in version 3.1.1
+
+- Reading raw files using xcmsSet or xcmsRaw uses now the automatic file type
+  detection feature from mzR.
+- c function to concatenate XCMSnExp objects.
+- groupnames method for XCMSnExp objects (issue #250).
+- Fix #237: findPeaks.MSW was not throwing an error if applied to multi-spectrum
+  MS file.
+- Fix #249: quantile call in adjustRtime PeakGroups without na.rm = TRUE.
+- Fix #259
+
+
+# xcms 2.99
+
+## Changes in version 2.99.10
+
+- Fix #230: Failing vignettes on Windows.
+
+## Changes in version 2.99.9
+
+- Chromatographic peak detection uses adjusted retention times on an aligned
+  XCMSnExp object (issue #213, #208).
+- New parameter msLevel for processHistory,XCMSnExp.
+- New parameter keepAdjustedRtime for filterMsLevel,XCMSnExp, dropChromPeaks,
+  XCMSnExp and dropFeatureDefinitions,XCMSnExp.
+- Add parameter msLevel to chromatogram,XCMSnExp method (issue #205).
+- Obiwarp alignment is now performed on one MS level and adjustment is applied
+  to all MS levels (issue #214).
+- Add function plotMsData to plot intensity against retention time and m/z
+  against retention time for a MS slice in one sample.
+- Add argument msLevel = 1L to extractMsData method (issue #223).
+- New applyAdjustedRtime function to consolidate the alignment results, i.e.
+  replace the raw retention times in the XCMSnExp with the adjusted retention
+  times.
+- [,XCMSnExp method gains argument keepAdjustedRtime to allow keeping adjusted
+  retention times in the sub-setting.
+- Implement spectrapply,XCMSnExp to ensure returned results use adjusted
+  retention times (if present).
+- [[,XCMSnExp method returns a Spectrum object with adjusted retention time, if
+  the XCMSnExp contains adjusted retention times.
+- Argument 'sampleGroups' is mandatory for 'PeakDensityParam' (issue #228).
+- Fix #191: Excessive memory use in fillPeaks.
+- Fix #220: peaks matrix is missing column "sample" if no peaks were found in
+  the first sample.
+- Fix #222: findChromPeaks does not return an XCMSnExp object filtered to a
+  single MS level despite peak detection is performed on a single level.
+- Fix problem in plotMsData causing wrong colors to be used to label the data
+  points.
+
+## Changes in version 2.99.8
+
+- Replace xcmsMSn Rnw with Rmd vignette to fix Windows build errors.
+
+## Changes in version 2.99.7
+
+- Fix #201: Warnings: 'readMSData2' is deprecated, thanks to L. Gatto.
+- Merge with BioC git after transition
+
+## Changes in version 2.99.6
+
+- calibrate,XCMSnExp method that allows to calibrate chromatographic peaks.
+- Export phenoDataFromPaths function (issue $195).
+- Add arguments mz and rt to featureDefinitions method allowing to extract
+  features within the specified ranges.
+- Increase n for the density function call in group density-based correspondence
+  by 2.
+- Replace xcmsDirect.Rnw with rmarkdown-based vignette using the new user
+  interface.
+- issue #196: removed the unnecessary requirement for same-dimension profile
+  matrices in adjustRtime,XCMSnExp,ObiwarpParam.
+- issue #194: fixes in retcor.obiwarp: 1) subset raw data if scanrange != NULL.
+  2) if the mz range of the two files to be aligned differ, expand them
+  correctly. Depending on the profStep and the mz values/ranges the matrices
+  were not expanded correctly.
+- Potential problems in the plotChromPeakDensity function.
+
+## Changes in version 2.99.5
+
+- Re-enable sleep parameter in findPeaks.centWave and findPeaks.matchedFilter.
+
+## Changes in version 2.99.4
+
+- Add plotChromPeaks function to plot the definition (rt and mz range) of
+  detected chromatographic peaks of one file into the mz-rt plane.
+- Add plotChromPeakImage function to plot the number of detected peaks along
+  the retention time axis per file as an image plot.
+- Move Chromatogram class and functionality to the MSnbase package
+- Add argument msLevel to the findChromPeaks method to allow (chromatographic)
+  peak detection also on MS level > 1.
+- Polarity information was not read from mzXML files (issue #192).
+
+## Changes in version 2.99.3
+
+- issue #188: determine file type from file content if file ending not known.
+
+## Changes in version 2.99.2
+
+- issue #181: problem when isCentroided,Spectrum method returns NA because of
+  too few peaks in a spectrum. Fixed by checking in such cases all spectra in
+  the file.
+- issue #184: add parameter sleep to do_groupChromPeaks_density function to be
+  backwards compatible with the old group.density code.
+
+## Changes in version 2.99.1
+
+- extractMsData to extract raw MS data as a data.frame (issue #120).
+- issue #175: an error is now thrown if no peak group was identified for peak
+  group retention time correction.
+- issue #178: scanrange was collapsed when the adjusted range was reported
+  (pull request by Jan Stanstrup).
+- issue #180: error when both parameters method and smooth are provided in the
+  retcor method.
+
+## Changes in version 2.99.0
+
+- plotChromatogram and highlightChromPeaks functions.
+- plotChromPeakDensity function.
+- clean method for Chromatogram classes.
+- Change default for ppm parameter in chromPeaks method to 0.
+- extractChromatograms supports extraction of multiple rt and mz ranges.
+- New parameter missing for extractChromatograms allowing to specify the
+  intensity value to be used for rts for which no signal is available within
+  the mz range.
+- extractChromatograms returns Chromatograms of length equal to the number of
+  scans within the specified rt range, even if no signals are measured
+  (intensity values are NA).
+
+
+# xcms 1.53
+
+## Changes in version 1.53.1
+
+- Increase parameter n for the density call in the peak density correspondence
+  method. This enables to separate neighboring peaks using small n (issue #161).
+  Thanks to Jan Stanstrup.
+
+# xcms 1.51
+
+## Changes in version 1.51.11
+
+- Parameter "filled" for featureValues (issue #157).
+- Parameters "rt" and "mz" in chromPeaks method allowing to extract
+  chromatographic peaks from the specified ranges (issue #156).
+- Fixed possible memory problem in obiwarp (issue #159).
+- Update getPeaks to use non-deprecated API (issue #163).
+
+## Changes in version 1.51.10
+
+- filterRt for Chromatogram class (issue #142).
+- adjustRtimePeakGroups function (issue #147).
+- adjustRtime,XCMSnExp,PeakGroupsParam and do_adjustRtime_peakGroups support
+  use of pre-defined matrix to perform alignment (issue #153).
+- plotAdjustedRtime to visualize alignment results (issue #141).
+- featureDefinitions and featureValues return DataFrame and matrix with rownames
+  corresponding to arbitrary feature IDs (issue #148).
+- New peakGroupsMatrix slot for PeakGroupsParam class (issue #153).
+- Issue #146: ensure adjusted retention times returned by the peakGroups method
+  to be in the same order than the raw retention times.
+
+## Changes in version 1.51.9
+
+- fillChromPeaks, dropFilledChromPeaks methods and FillChromPeaksParam class.
+- featureValues method.
+- Extended new_functionality vignette.
+- Change default backend for reading mzML files to pwiz.
+- Issue #135: fix peak signal integration for centWave.
+- Issue #139: problem with expand.mz and expand.rt in fillPeaks.chrom.
+- Issue #137: Error in findChromPeaks if no peaks are found.
+
+## Changes in version 1.51.8
+
+- Add Chromatogram class and extractChromatograms method.
+- Issue #118: failing unit test on Windows build machine.
+- Issue #133: error with c() and xcmsSet without peaks.
+- Issue #134: xcmsSet constructor endless loop.
+
+## Changes in version 1.51.7
+
+- Major renaming of methods and classes to follow the naming convention:
+  - chromatographic peak (chromPeak): the peaks identified in rt dimension.
+  - feature: mz-rt feature, being the grouped chromatographic peaks within and
+    across samples.
+- Issue #127: failing unit test on Windows build machine.
+
+## Changes in version 1.51.6
+
+- groupFeatures and adjustRtime methods for XCMSnExp objects.
+- New Param classes for groupFeatures and adjustRtime analysis methods:
+  FeatureDensityParam, MzClustParam, NearestFeaturesParam, FeatureGroupsParam
+  and ObiwarpParam.
+- Issue #124 (filterRt,XCMSnExp returned empty object).
+
+## Changes in version 1.51.5
+
+- MsFeatureData and XCMSnExp objects.
+- features, features<-, adjustedRtime, adjustedRtime<-, featureGroups,
+  featureGroups<-, hasAlignedFeatures, hasAdjustedRtime and hasDetectedFeatures
+  methods.
+- dropFeatures, dropFeatureGroups and dropAdjustedRtime methods.
+- filterMz, filterRt, filterFile etc implemented.
+- mz, intensity and rtime methods for XCMSnExp allowing to return values grouped
+  by sample.
+- Issue #99 (rtrange outside of retention time range in getEIC,xcmsSet).
+- Issue #101 (xcmsRaw function returns NULL if mslevel = 1 is specified).
+- Issue #102 (centWave returns empty matrix if scales not OK). Thanks to
+  J. Stanstrup.
+- Issue #91 (warning instead of error if no peaks in ROI). Thanks to J. Stanstrup.
+
+## Changes in version 1.51.4
+
+- added deepCopy to avoid corrupting the original object, thanks to
+  J. Stanstrup, closes #93
+
+## Changes in version 1.51.3
+
+- binYonX binning function.
+- imputeLinInterpol function providing linear interpolation of missing values.
+- breaks_on_binSize and breaks_on_nBins functions to calculate breaks defining
+  bins.
+- New vignette "new_functionality.Rmd" describing new and modified functionality
+  in xcms.
+- Add do_detectFeatures_matchedFilter function.
+- Add do_detectFeatures_centWave function.
+- Add do_detectFeatures_centWaveWithPredIsoROIs function and unit test.
+- Implement a new data import function.
+- Add do_detectFeatures_MSW function and unit test.
+- Argument stopOnError in xcmsSet function that allows to perform feature
+  detection on all files without stopping on errors.
+- Method showError for xcmsSet objects that list all errors during feature
+  detection (if stopOnError = FALSE in the xcmsSet function).
+- [ method to subset xcmsRaw objects by scans.
+- profMat method to extract/create the profile matrix from/for an xcmsRaw.
+- Add new detectFeatures methods for MSnExp and OnDiskMSnExp objects from the
+  MSnbase package.
+- Add new CentWaveParam, MatchedFilterParam, MassifquantParam, MSWParam and
+  CentWavePredIsoParam parameter class to perform method dispatch in the
+  detectFeatures method.
+- retcor.obiwarp uses the new binning methods for profile matrix generation.
+- scanrange,xcmsRaw reports always a scanrange of 1 and length(object@scantime).
+- scanrange,xcmsSet reports the scanrange eventually specified by the user in
+  the xcmsSet function.
+- Fixed bug in rawMat (issue #58).
+- Fix issue #60: findPeaks.massifquant always returns a xcmsPeaks object.
+
+## Changes in version 1.51.2
+
+- As suggested by Jan Stanstrup, do not error if a centWave ROI
+  contains no data, closes #90
+
+## Changes in version 1.51.1
+
+- Fix incorrrect indexing getEIC function reported by Will Edmands, closes #92
+
+
+# xcms 1.49
+
+## Changes in version 1.49.7
+
+- Fix documentation warnings.
+
+## Changes in version 1.49.6
+
+- Peak Picking function findPeaks.centWaveWithPredictedIsotopeROIs() and
+  findPeaks.addPredictedIsotopeFeatures(), which allow more sensitive detection
+  of isotope features.
+
+## Changes in version 1.49.5
+
+- Some documentation updates.
+- Preparation for a new binning function
+
+## Changes in version 1.49.4
+
+- Fix getXcmsRaw that would prevent retention time correction to be applied
+  (issue #44 reported by Aleksandr).
+
+## Changes in version 1.49.3
+
+- updateObject method for xcmsSet.
+- xcms uses now BiocParallel for parallel processing. All other parallel
+  processing functions have been deprecated.
+- Added missing package imports.
+- Fix bug in fillPeaksChromPar referencing a non-existing variables i and
+  object.
+- Fix bug in group.nearest: variable scoreList was mis-spelled (coreList).
+- Remove all DUP = FALSE from the .C calls as they are ignored anyways.
+- Re-organization of class, function and method definitions in R-files.
+- Use roxygen2 to manage the DESCRIPTION's collate field.
+
+## Changes in version 1.49.2
+
+- Initial support for exporint mzTab format. Since Changes are
+  still to be expected, xcms:::writeMzTab() is not yet exported.
+
+## Changes in version 1.49.1
+
+- The raw CDF/mzXML/mzData/mzML is assumed to have scans sorted by m/z.
+  Instead of throwing an "m/z sort assumption violated !" error,
+  the data is re-read and on-demand sorted by m/z.
+
+
+# xcms 1.47
+
+## Changes in version 1.47.3
+
+- Disable parallel processing in unit tests causing a timeout
+  on BioC build machines
+
+## Changes in version 1.47.2
+
+- Fix problem in getEIC on xcmsSet objects reported by Alan Smith in issue #7 and
+  add a RUnit test case to test for this (test.issue7 in runit.getEIC.R).
+- Changed some unnecessary warnings into messages.
+
+## Changes in version 1.47.2
+
+- Disabled parallel processing in unit tests
+- migrate dependencies from ncdf -> ncdf4
+
+
+# xcms 1.45
+
+## Changes in version 1.45.7
+
+- Disabled Rmpi support and usage on Windows
+
+## Changes in version 1.45.6
+
+- J. Rainer implemented a [ method that allows to subset an xcmsSet.
+- Fixed a problem in split.xcmsSet that did not split the phenoData properly.
+  Added some details to the documentation of xcmsSet-class.
+
+## Changes in version 1.45.5
+
+- The sampclass method for xcmsSet will now return the content of the
+  column "class" from the data.frame in the phenoData slot, or if not
+  present, the interaction of all factors (columns) of that data.frame.
+- The sampclass<- method replaces the content of the "class" column in
+  the phenoData data.frame. If a data.frame is submitted, the interaction
+  of its columns is calculated and stored into the "class" column.
+- Fixed a bug that resulted in a cryptic error message
+  when no input files are available to the xcmsSet function.
+
+## Changes in version 1.45.4
+
+- Fixed a bug in the levelplot method for xcmsSet.
+
+## Changes in version 1.45.3
+
+- xcmsSet now allows phenoData to be an AnnotatedDataFrame.
+- new slots for xcmsRaw:
+  - mslevel: store the mslevel parameter submitted to xcmsRaw.
+  - scanrange: store the scanrange parameter submitted to xcmsRaw.
+- new slots for xcmsSet:
+  - mslevel: stores the mslevel argument from the xcmsSet method.
+  - scanrange: to keep track of the scanrange argument of the xcmsSet method.
+- new methods for xcmsRaw:
+  - levelplot: similar to the image method, plots m/z vs RT with color coded
+    intensities.
+  - mslevel: returns the value for the .mslevel slot. For downstream
+    compatibility, this method returns NULL if the object does not have the same
+    named slot.
+  - profinfo: same functionality as the profinfo method for xcmsSet.
+  - scanrange: returns the value for the scanrange slot. For downstream
+    compatibility, this method returns NULL if the object does not have the same
+    named slot.
+- new methods for xcmsSet:
+  - getXcmsRaw: returns a xcmsRaw object for one or more files in the xcmsSet,
+    eventually applying retention time correction etc.
+  - levelplot: similar to the image method, plots m/z vs RT with color coded
+    intensities. Allows in addition to highlight identified peaks.
+  - mslevel: returns the value for the mslevel slot. For downstream
+    compatibility, this method returns NULL if the object does not have the same
+    named slot.
+  - profMethod: same functionality as the profMethod method of xcmsRaw.
+  - profStep: same functionality as the profStep method of xcmsRaw.
+  - scanrange: returns the value for the scanrange slot. For downstream
+    compatibility, this method returns NULL if the object does not have the same
+    named slot.
+- show method for xcmsSet updated to display also informations about the mslevel
+  and scanrange.
+- Elaborated some documentation entries.
+- rtrange and mzrange for xcmsRaw method plotEIC use by default the full RT and
+  m/z range.
+- Added arguments "lty" and "add" to plotEIC method for xcmsRaw.
+- getEIC without specifying mzrange returns the ion chromatogram for the full
+  m/z range (i.e. the base peak chromatogram).
+- Checking if phenoData is a data.frame or AnnotatedDataFrame and throw an error
+  otherwise.
+- xcmsSet getEIC method for water Lock mass corrected files for a subset of
+  files did not evaluate whether the specified files were corrected.
+
+## Changes in version 1.45.2
+
+- The xcms split() function now accepts factors that are shorter than the number
+  of samples in the xcmsSet, following more closely the standard split()
+  behaviour
+
+## Changes in version 1.45.1
+
+- plotrt now allows col to be a vector of color definition,
+  same as the plots for retcor methods.
+- Added $ method to access phenoData columns in a eSet/ExpressionSet like
+  manner.
+- Allow to use the "parallel" package for parallel processing of the functions
+  xcmsSet and fillPeaks.chrom.
+- Thanks to J. Rainer!
+
+
+# xcms 1.43
+
+## Changes in version 1.43.3
+
+- Give a more verbose error message when file not found
+
+## Changes in version 1.43.2
+
+- Use ProtGenerics, adapted xcms peaks()
+
+## Changes in version 1.43.1
+
+- function plotQC() for plotting various QC plots on RT and m/z
+
+
+# xcms 1.41
+
+## Changes in version 1.41.1
+
+- fix sampclass generation from phenoData if some combinations of factors don't
+  exist
+- disable parallel code in manpages to avoid issues on BioC windows build farm
+  machines
+
+
+# xcms 1.39
+
+## Changes in version 1.39.6
+
+- Massifquant reports the maximum intensity for each isotope trace (peak). This
+  is useful for interactive parameter optimization.
+- Major memory reduction in parallel fillPeaks() thanks to Jan Stanstrup. Now
+  using an environment to mirror gvals to each list item in the very large
+  argList.
+
+## Changes in version 1.39.4
+
+- Fixed write.cdf(), which had an intensity offset of +1, added a unit test
+
+## Changes in version 1.39.3
+
+- New R-devel check unload better. Lingering ramp code removed, import from
+  mzR. Cleaned up other errors in package check.
+
+## Changes in version 1.39.1
+
+- Updated doubleMatrix c code to allow for larger profile matrixes
+- Moved inst/doc to vignettes
+
+
+# xcms 1.37
+
+## Changes in version 1.37.6
+
+- Introducing write.mzQuantML(xcmsSet) to export the peak list and grouped
+  matrix to the PSI format mzQuantML (see http://www.psidev.info/mzquantml)
+- Add Brigham Young University to LICENSE file for copyright purposes.
+- Add copyright information display when running findPeaks.massifquant()
+  within xcmsRaw.R
+- Clean and update documentation for findPeaks.massifquant-methods.Rd
+- Remove unused parameters in findKalmanROIs() within xcmsRaw.R
+
+## Changes in version 1.37.5
+
+- fixed bug in retcor.obiwarp where the scanrange of the first sample would be
+  checked instead of the center sample
+
+## Changes in version 1.37.4
+
+- Skip t-test in diffreport() if one class has less than 2 samples.
+
+## Changes in version 1.37.3
+
+- fixed bug in patternVsRowScore (group.nearest) that was introduced by the
+  modifications in rev 65169 and caused features to be aligned that were far
+  outside the given m/z and retention time windows.
+
+## Changes in version 1.37.1
+
+- fixed fillPeaks, which 1) dropped non-standard columns and 2) failed if
+  nothing to do, based on patches by Tony Larson.
+
+## Changes in version 1.37.1
+
+- Introducing msn2xcmsRaw, to allow findPeaks() on MS2 and MSn data
+
+
+# xcms 1.35
+
+## Changes in version 1.35.7
+
+- fixed indexing bug in group.nearest, which under certain circumstances caused
+  all peaks in the first sample to be ignored (reported by Tony Larson)
+
+## Changes in version 1.35.6
+
+- Obiwarp retention time alignment error-ed if scanrange was used as a parameter
+  setting during xcmsSet/peak detection The method now tries to automatically
+  find the set scanrange and uses this range for alignment.
+
+## Changes in version 1.35.4
+
+- Introducing parallel fillPeaks
+- Replace snow requirement with minimum R version 2.14.0
+
+## Changes in version 1.35.3
+
+- if group.density was used with very low minfrac settings (< 0.5) it did not
+  return all feature groups, but only those that include features from at least
+  50% of samples in a group. This limitation was removed.
+
+## Changes in version 1.35.2
+
+- Behind the scenes xcms now uses the xcmsSource class to read raw data.  This
+  allows e.g. to write a class that pulls raw data from e.g. a database
+- massifquant: simplified logic structure of Tracker::claimDataIdx resolved
+  failure on new test case.
+- massifquant: reporting features data structure compatible with multiple sample
+  comparison within XCMS.
+
+## Changes in version 1.35.1
+
+- The mzData export is now much faster and uses less memory
+
+
+# xcms 1.33
+
+## Changes in version 1.33.16
+
+- diffreport and plotEIC have a new parameter mzdec, with is the number of
+  decimal places of the m/z values in the EIC plot title
+
+## Changes in version 1.33.16
+
+- Lock mass gap filler now works with netCDF lock mass function file to find the
+  exact times of the scans and works with the newer Waters MS instruments.
+
+## Changes in version 1.33.15
+
+- scanrage is now honoured in xcmsSet, also when in parallel mode
+
+## Changes in version 1.33.14
+
+- scanrage is now honoured in xcmsRaw, and consequently also in
+  xcmsSet(matchedFilter), where previously it was ignored.
+
+## Changes in version 1.33.13
+
+- write.cdf() has been fixed to write files AMDIS can read
+
+## Changes in version 1.33.12
+
+- write.mzData adds Polarity to the file if available
+
+## Changes in version 1.33.11
+
+- centWave uses a new method to estimate local noise which improves detection of
+  closely spaced peaks
+- group.mzClust was failing when result had one peak
+
+# xcms 1.32 and before
+
+For more details and all changes before May 2012 please see the (now
+discontinued) CHANGELOG in the source package (inst/ folder).
+
+## CHANGED BEHAVIOUR since Version 1.32:
+
+Other Changes since Version 1.32:
+- improved mzData writing, now includes MSn spectra and less verbose.
+- improved netCDF writing, but not yet good enough for AMDIS
+
+## CHANGED BEHAVIOUR since Version 1.14:
+
+- centWave may report a smaller set of peaks, due to a small bug
+  in the ROI algorithm some features with mass deviation > ppm were retained.
+
+Other Changes since Version 1.14:
+
+- New method for grouping: an algorithm inspired by mzMine
+  group(method="nearest") has been implemented. It is slower
+  than group(method="density"). It can individually group
+  close-eluting peaks of very similar mass
+
+- New method for retention time correction:
+  The retcor(method="obiwarp") algorithm operates on the raw data,
+  and thus allows to correct runs without well-behaving
+  peak groups, or without peak picking at all.
+
+- fillPeaks(method="MSW") is now also available
+  for direct infusion spectra. The findPeaks(method="MSW")
+  now returns several intensities, and correctly reports
+  mzmin and mzmax for peaks.
+
+- centWave now uses dynamic memory allocation, needs much less memory,
+  and these BUF related errors should be a thing of the past.
+
+- centWave gains an optional argument "noise",
+  which is useful for data that was centroided without any intensity threshold,
+  centroids with intensity < "noise" are omitted from ROI detection
+
+- the fillPeaks() methods now remember which was
+  an observed, and which was a "filled" peak.
+
+- For direct infusion spectra diffreport() now shows
+  the raw peak shapes, and also indicated "real" and "filled" peaks.
+
+- xcmsRaw can now filter for positive/negative spectra,
+  if the file includes both polarities. xcmsSet() can pass
+  the polarity to contain positive/negative peaks only.
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 7e4f257cf..2d69b37bf 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -331,6 +331,9 @@ setGeneric("checkBack<-", function(object, value) standardGeneric("checkBack<-")
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
+#' library(xcms)
+#' library(MsExperiment)
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
 #' ## Get EICs for every detected chromatographic peak
@@ -708,6 +711,8 @@ setGeneric("family<-", function(object, value) standardGeneric("family<-"))
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(xcms)
+#' library(MsExperiment)
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
 #' ## Disable parallel processing for this example
@@ -1009,6 +1014,8 @@ setGeneric("filepaths<-", function(object, value) standardGeneric("filepaths<-")
 #' @examples
 #'
 #' ## Load a test data set with identified chromatographic peaks
+#' library(xcms)
+#' library(MsExperiment)
 #' res <- loadXcmsData("faahko_sub2")
 #'
 #' ## Disable parallel processing for this example
@@ -1016,7 +1023,7 @@ setGeneric("filepaths<-", function(object, value) standardGeneric("filepaths<-")
 #'
 #' ## Perform the correspondence. We assign all samples to the same group.
 #' res <- groupChromPeaks(res,
-#'     param = PeakDensityParam(sampleGroups = rep(1, length(fileNames(res)))))
+#'     param = PeakDensityParam(sampleGroups = rep(1, length(res))))
 #'
 #' ## For how many features do we lack an integrated peak signal?
 #' sum(is.na(featureValues(res)))
@@ -1388,6 +1395,8 @@ setGeneric("group", function(object, ...) standardGeneric("group"))
 #'
 #' @param value Replacement value for `<-` methods.
 #'
+#' @param x The parameter object.
+#'
 #' @param ... Optional parameters.
 #'
 #' @return For `groupChromPeaks`: either an [XcmsExperiment()] or [XCMSnExp()]
@@ -1905,6 +1914,8 @@ setGeneric("reconstructChromPeakSpectra", function(object, ...)
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(xcms)
+#' library(MsExperiment)
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
 #' ## Disable parallel processing for this example
@@ -2055,6 +2066,8 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(xcms)
+#' library(MsExperiment)
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
 #' ## Set up parameter to save as .RData file
diff --git a/R/DataClasses.R b/R/DataClasses.R
index af46beb80..fab0cc414 100644
--- a/R/DataClasses.R
+++ b/R/DataClasses.R
@@ -452,6 +452,8 @@ setClass("XProcessHistory",
 #' bell curve. See https://github.com/sneumann/xcms/pull/685 and
 #' https://doi.org/10.1186/s12859-023-05533-4 for more information.
 #'
+#' @param x The parameter object.
+#'
 #' @details
 #'
 #' The centWave algorithm is most suitable for high resolution
@@ -487,7 +489,7 @@ setClass("XProcessHistory",
 #' detection in purely chromatographic data.
 #'
 #' @references
-#' Ralf Tautenhahn, Christoph B\"{o}ttcher, and Steffen Neumann "Highly
+#' Ralf Tautenhahn, Christoph Böttcher, and Steffen Neumann "Highly
 #' sensitive feature detection for high resolution LC/MS" \emph{BMC Bioinformatics}
 #' 2008, 9:504
 #'
@@ -517,13 +519,14 @@ NULL
 #' cwp
 #'
 #' ## Perform the peak detection using centWave on some of the files from the
-#' ## faahKO package. Files are read using the readMSData from the MSnbase
-#' ## package
+#' ## faahKO package. Files are read using the `readMsExperiment` function
+#' ## from the MsExperiment package
 #' library(faahKO)
 #' library(xcms)
+#' library(MsExperiment)
 #' fls <- dir(system.file("cdf/KO", package = "faahKO"), recursive = TRUE,
 #'            full.names = TRUE)
-#' raw_data <- readMSData(fls[1], mode = "onDisk")
+#' raw_data <- readMsExperiment(fls[1])
 #'
 #' ## Perform the peak detection using the settings defined above.
 #' res <- findChromPeaks(raw_data, param = cwp)
@@ -892,7 +895,7 @@ setClass("MatchedFilterParam",
 #'     centWave algorithm, which includes wavelet estimation.
 #'
 #' @details This algorithm's performance has been tested rigorously
-#'     on high resolution LC/{OrbiTrap, TOF}-MS data in centroid mode.
+#'     on high resolution LC/(OrbiTrap, TOF)-MS data in centroid mode.
 #'     Simultaneous kalman filters identify chromatographic peaks and calculate
 #'     their area under the curve. The default parameters are set to operate on
 #'     a complex LC-MS Orbitrap sample. Users will find it useful to do some
@@ -1108,6 +1111,7 @@ NULL
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' ## Create a MSWParam object
 #' mp <- MSWParam()
 #' ## Change snthresh parameter
@@ -1836,6 +1840,7 @@ setClass("MsFeatureData", contains = c("environment"),
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
diff --git a/R/do_findChromPeaks-functions.R b/R/do_findChromPeaks-functions.R
index cb89383e2..9767c8f06 100644
--- a/R/do_findChromPeaks-functions.R
+++ b/R/do_findChromPeaks-functions.R
@@ -68,7 +68,8 @@
 #' @family core peak detection functions
 #'
 #' @references
-#' Ralf Tautenhahn, Christoph B\"{o}ttcher, and Steffen Neumann "Highly
+#'
+#' Ralf Tautenhahn, Christoph Böttcher, and Steffen Neumann "Highly
 #'     sensitive feature detection for high resolution LC/MS"
 #'     \emph{BMC Bioinformatics} 2008, 9:504
 #'
@@ -163,7 +164,7 @@ do_findChromPeaks_centWave <- function(mz, int, scantime, valsPerSpect,
                        verboseColumns = verboseColumns, roiList = roiList,
                        firstBaselineCheck = firstBaselineCheck,
                        roiScales = roiScales, sleep = sleep,
-                       extendLengthMSW = extendLengthMSW, 
+                       extendLengthMSW = extendLengthMSW,
                        verboseBetaColumns = verboseBetaColumns)
     } else {
         ## message("DEBUG: using modified centWave.")
@@ -579,7 +580,7 @@ do_findChromPeaks_centWave <- function(mz, int, scantime, valsPerSpect,
                 lm <- .narrow_rt_boundaries(lm, d)
                 lm_seq <- lm[1]:lm[2]
                 pd <- d[lm_seq]
-                
+
                 # Implement a fit of a skewed gaussian (beta distribution)
                 # for peak shape and within-peak signal-to-noise ratio
                 # See https://doi.org/10.1186/s12859-023-05533-4 and
@@ -1265,7 +1266,7 @@ do_findChromPeaks_centWave <- function(mz, int, scantime, valsPerSpect,
 #'     by specifying \code{withWave = TRUE}.
 #'
 #' @details This algorithm's performance has been tested rigorously
-#'     on high resolution LC/{OrbiTrap, TOF}-MS data in centroid mode.
+#'     on high resolution LC/(OrbiTrap, TOF)-MS data in centroid mode.
 #'     Simultaneous kalman filters identify peaks and calculate their
 #'     area under the curve. The default parameters are set to operate on
 #'     a complex LC-MS Orbitrap sample. Users will find it useful to do some
@@ -2673,7 +2674,7 @@ do_findChromPeaks_centWaveWithPredIsoROIs <-
              verboseColumns = FALSE, roiList = list(),
              firstBaselineCheck = TRUE, roiScales = NULL, snthreshIsoROIs = 6.25,
              maxCharge = 3, maxIso = 5, mzIntervalExtension = TRUE,
-             polarity = "unknown", extendLengthMSW = FALSE, 
+             polarity = "unknown", extendLengthMSW = FALSE,
              verboseBetaColumns = FALSE) {
         ## Input argument checking: most of it will be done in
         ## do_findChromPeaks_centWave
@@ -3271,9 +3272,9 @@ peaksWithMatchedFilter <- function(int, rt, fwhm = 30, sigma = fwhm / 2.3548,
 #' @examples
 #'
 #' ## Reading a file
+#' library(MsExperiment)
 #' library(xcms)
-#' od <- readMSData(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
-#'     mode = "onDisk")
+#' od <- readMsExperiment(system.file("cdf/KO/ko15.CDF", package = "faahKO"))
 #'
 #' ## Extract chromatographic data for a small m/z range
 #' mzr <- c(272.1, 272.2)
@@ -3633,9 +3634,9 @@ peaksWithCentWave <- function(int, rt,
 #'
 #' @examples
 #'
+#' library(MsExperiment)
 #' library(xcms)
-#' od <- readMSData(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
-#'     mode = "onDisk")
+#' od <- readMsExperiment(system.file("cdf/KO/ko15.CDF", package = "faahKO"))
 #'
 #' ## Extract chromatographic data for a small m/z range
 #' chr <- chromatogram(od, mz = c(272.1, 272.3))[1, 1]
@@ -3731,7 +3732,7 @@ peaksWithCentWave <- function(int, rt,
 #' @author William Kumler
 #'
 #' @noRd
-.get_beta_values <- function(intensity, rtime = seq_along(intensity), 
+.get_beta_values <- function(intensity, rtime = seq_along(intensity),
                              skews=c(3, 3.5, 4, 4.5, 5), zero.rm = TRUE){
   if (zero.rm) {
     ## remove 0 or NA intensities
@@ -3744,7 +3745,7 @@ peaksWithCentWave <- function(int, rt,
     beta_snr <- NA
   } else {
     beta_sequence <- rep(.scale_zero_one(rtime), each=length(skews))
-    beta_vals <- t(matrix(dbeta(beta_sequence, shape1 = skews, shape2 = 5), 
+    beta_vals <- t(matrix(dbeta(beta_sequence, shape1 = skews, shape2 = 5),
                           nrow = length(skews)))
     # matplot(beta_vals)
     beta_cors <- cor(intensity, beta_vals)
diff --git a/R/do_groupChromPeaks-functions.R b/R/do_groupChromPeaks-functions.R
index 9bf3668bc..1170ef44d 100644
--- a/R/do_groupChromPeaks-functions.R
+++ b/R/do_groupChromPeaks-functions.R
@@ -75,6 +75,8 @@
 #'
 #' @examples
 #' ## Load the test file
+#' library(xcms)
+#' library(MsExperiment)
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
 #' ## Disable parallel processing for this example
diff --git a/R/functions-Chromatogram.R b/R/functions-Chromatogram.R
index 0cede6580..6e90531de 100644
--- a/R/functions-Chromatogram.R
+++ b/R/functions-Chromatogram.R
@@ -62,8 +62,8 @@
 #'
 #' @examples
 #'
-#' xd <- readMSData(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
-#'     mode = "onDisk")
+#' library(MsExperiment)
+#' xd <- readMsExperiment(system.file('cdf/KO/ko15.CDF', package = "faahKO"))
 #' chr <- chromatogram(xd, mz = c(-0.5, 0.5) + 453.2)
 #' xchr <- findChromPeaks(chr, param = CentWaveParam(snthresh = 0))
 #' plot(xchr)
diff --git a/R/functions-OnDiskMSnExp.R b/R/functions-OnDiskMSnExp.R
index d0c16d5e4..b774b4000 100644
--- a/R/functions-OnDiskMSnExp.R
+++ b/R/functions-OnDiskMSnExp.R
@@ -703,6 +703,7 @@ setReplaceMethod("dirname", "OnDiskMSnExp", function(path, value) {
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
 #' pest_dda <- readMSData(fl, mode = "onDisk")
 #' res <- .estimate_prec_intensity(pest_dda)
diff --git a/R/functions-XCMSnExp.R b/R/functions-XCMSnExp.R
index fdbf738c7..2bd445721 100644
--- a/R/functions-XCMSnExp.R
+++ b/R/functions-XCMSnExp.R
@@ -796,6 +796,7 @@ adjustRtimePeakGroups <- function(object, param = PeakGroupsParam(),
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
@@ -964,6 +965,7 @@ isCalibrated <- function(object) {
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
@@ -1202,6 +1204,7 @@ featureSummary <- function(x, group, perSampleCounts = FALSE,
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
@@ -1854,6 +1857,7 @@ setMethod("hasFilledChromPeaks", "XCMSnExp", function(object) {
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' xd <- readMSData(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
 #'     mode = "onDisk")
 #' xd <- findChromPeaks(xd, param = CentWaveParam())
diff --git a/R/functions-XChromatogram.R b/R/functions-XChromatogram.R
index bfdd1f47c..b17f591dd 100644
--- a/R/functions-XChromatogram.R
+++ b/R/functions-XChromatogram.R
@@ -141,6 +141,7 @@
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' ## Create a XChromatogram object
 #' pks <- matrix(nrow = 1, ncol = 6)
 #' colnames(pks) <- c("rt", "rtmin", "rtmax", "into", "maxo", "sn")
diff --git a/R/functions-XChromatograms.R b/R/functions-XChromatograms.R
index 3f41fa408..119a29a71 100644
--- a/R/functions-XChromatograms.R
+++ b/R/functions-XChromatograms.R
@@ -43,6 +43,7 @@
 #' ## ---- Creation of XChromatograms ----
 #' ##
 #' ## Create a XChromatograms from Chromatogram objects
+#' library(MSnbase)
 #' dta <- list(Chromatogram(rtime = 1:7, c(3, 4, 6, 12, 8, 3, 2)),
 #'     Chromatogram(1:10, c(4, 6, 3, 4, 7, 13, 43, 34, 23, 9)))
 #'
diff --git a/R/functions-imputation.R b/R/functions-imputation.R
index 9ae458329..3475db216 100644
--- a/R/functions-imputation.R
+++ b/R/functions-imputation.R
@@ -22,6 +22,7 @@
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' library(faahKO)
 #' data("faahko")
 #'
@@ -111,6 +112,7 @@ imputeRowMin <- function(x, min_fraction = 1/2) {
 #' @examples
 #'
 #' library(faahKO)
+#' library(MSnbase)
 #' data("faahko")
 #'
 #' xset <- group(faahko)
diff --git a/R/functions-utils.R b/R/functions-utils.R
index 8df509b18..77d236ebf 100644
--- a/R/functions-utils.R
+++ b/R/functions-utils.R
@@ -307,8 +307,9 @@ weightedMeanAroundApex <- function(x, w = rep(1, length(x)), i = 1) {
 #'
 #' @description
 #'
-#' **UPDATE**: please use `plot(x, type = "XIC")` from the `MSnbase` package
-#' instead. See examples below.
+#' **UPDATE**: please use `plot()` from the `MsExperiment` or
+#' `plot(x, type = "XIC")` from the `MSnbase` package instead. See examples
+#' in the vignette for more information.
 #'
 #' The `plotMsData` creates a plot that combines an (base peak )
 #' extracted ion chromatogram on top (rt against intensity) and a plot of
@@ -338,19 +339,6 @@ weightedMeanAroundApex <- function(x, w = rep(1, length(x)), i = 1) {
 #'
 #' @md
 #'
-#' @examples
-#'
-#' ## Read two files from the faahKO package
-#' library(faahKO)
-#' cdfs <- dir(system.file("cdf", package = "faahKO"), full.names = TRUE,
-#'     recursive = TRUE)[1:2]
-#' raw_data <- readMSData(cdfs, mode = "onDisk")
-#'
-#' ## Subset the object to a rt and mz range and plot the data.
-#' raw_data |>
-#'     filterRt(rt = c(2700, 2900)) |>
-#'     filterMz(mz = c(334.9, 335.1)) |>
-#'     plot(type = "XIC")
 plotMsData <- function(x, main = "", cex = 1, mfrow = c(2, 1),
                        grid.color = "lightgrey",
                        colramp = colorRampPalette(
diff --git a/R/functions-xcmsSet.R b/R/functions-xcmsSet.R
index 8eea47700..373ee20f0 100644
--- a/R/functions-xcmsSet.R
+++ b/R/functions-xcmsSet.R
@@ -418,12 +418,15 @@ phenoDataFromPaths <- function(paths) {
 ## patternVsRowScore
 patternVsRowScore <- function(currPeak, parameters, mplenv)
 {
+    if (!requireNamespace("RANN", quietly = TRUE))
+        stop("The use of 'patternVsRowScore' requires package 'RANN'. Please ",
+             "install with 'BiocInstaller::install(\"RANN\")'")
     mplistmeanCurr <- mplenv$mplistmean[, c("mz", "rt")]
     mplistmeanCurr[, "mz"] <- mplistmeanCurr[, "mz"] * parameters$mzVsRTBalance
     peakmatCurr <- mplenv$peakmat[currPeak, c("mz", "rt"), drop = FALSE]
     peakmatCurr[, "mz"] <- peakmatCurr[, "mz"] * parameters$mzVsRTBalance
 
-    nnDist <- nn2(mplistmeanCurr, peakmatCurr[, c("mz", "rt"), drop = FALSE],
+    nnDist <- RANN::nn2(mplistmeanCurr, peakmatCurr[, c("mz", "rt"), drop = FALSE],
                   k = min(length(mplistmeanCurr[, 1]), parameters$knn))
 
     scoreListcurr <- data.frame(score = numeric(0),
diff --git a/R/methods-Chromatogram.R b/R/methods-Chromatogram.R
index f2b7463fa..cdff7f10a 100644
--- a/R/methods-Chromatogram.R
+++ b/R/methods-Chromatogram.R
@@ -45,6 +45,7 @@
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' ## Loading a test data set with identified chromatographic peaks
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #' faahko_sub <- filterRt(faahko_sub, c(2500, 3700))
@@ -192,6 +193,7 @@ setMethod("findChromPeaks", signature(object = "Chromatogram",
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' chr1 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
 #'     intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))
 #' chr2 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
@@ -261,6 +263,7 @@ setMethod("correlate", signature = c(x = "Chromatogram", y = "Chromatogram"),
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' chr <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
 #'     intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))
 #'
diff --git a/R/methods-MChromatograms.R b/R/methods-MChromatograms.R
index 0b7f13e5c..78bd598ff 100644
--- a/R/methods-MChromatograms.R
+++ b/R/methods-MChromatograms.R
@@ -4,11 +4,14 @@
 #'
 #' @examples
 #'
+#' library(MsExperiment)
+#' library(xcms)
 #' ## Perform peak detection on an MChromatograms object
-#' od3 <- readMSData(c(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
+#'
+#' fls <- c(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
 #'     system.file("cdf/KO/ko16.CDF", package = "faahKO"),
-#'     system.file("cdf/KO/ko18.CDF", package = "faahKO")),
-#'     mode = "onDisk")
+#'     system.file("cdf/KO/ko18.CDF", package = "faahKO"))
+#' od3 <- readMsExperiment(fls)
 #'
 #' ## Disable parallel processing for this example
 #' register(SerialParam())
@@ -190,6 +193,7 @@ setMethod("removeIntensity", "MChromatograms",
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' chr1 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
 #'     intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))
 #' chr2 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
@@ -365,6 +369,7 @@ setMethod("filterColumnsKeepTop", "MChromatograms",
 #'
 #' ## Load preprocessed data and extract EICs for some features.
 #' library(xcms)
+#' library(MSnbase)
 #' xdata <- loadXcmsData()
 #' data(xdata)
 #' ## Update the path to the files for the local system
diff --git a/R/methods-Params.R b/R/methods-Params.R
index 0843298c8..e08ffda42 100644
--- a/R/methods-Params.R
+++ b/R/methods-Params.R
@@ -1498,3 +1498,15 @@ setReplaceMethod("ppm", "FillChromPeaksParam", function(object, value) {
     if (validObject(object))
         return(object)
 })
+
+#' @rdname findChromPeaks-centWave
+setMethod("as.list", "CentWaveParam", function(x, ...) {
+    x <- updateObject(x)
+    callNextMethod(x)
+})
+
+#' @rdname groupChromPeaks
+setMethod("as.list", "PeakDensityParam", function(x, ...) {
+    x <- updateObject(x)
+    callNextMethod(x)
+})
diff --git a/R/methods-XCMSnExp.R b/R/methods-XCMSnExp.R
index 449a5f4a2..516e8e3f4 100644
--- a/R/methods-XCMSnExp.R
+++ b/R/methods-XCMSnExp.R
@@ -947,6 +947,7 @@ setMethod("dropAdjustedRtime", "XCMSnExp", function(object) {
 #' @examples
 #'
 #' ## Loading a test data set with identified chromatographic peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
@@ -2085,6 +2086,7 @@ setMethod("featureValues", "XCMSnExp", function(object, method = c("medret",
 #' @examples
 #'
 #' ## Load a test data set with identified chromatographic peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
@@ -2799,6 +2801,7 @@ setMethod("dropFilledChromPeaks", "XCMSnExp", function(object) {
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
@@ -3169,6 +3172,7 @@ setMethod("writeMSData", signature(object = "XCMSnExp", file = "character"),
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
diff --git a/R/methods-group-features.R b/R/methods-group-features.R
index d27b15b69..eb7482821 100644
--- a/R/methods-group-features.R
+++ b/R/methods-group-features.R
@@ -126,6 +126,7 @@ setReplaceMethod("featureGroups", "XcmsResult", function(object, value) {
 #' @examples
 #'
 #' library(MsFeatures)
+#' library(MsExperiment)
 #' ## Load a test data set with detected peaks
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
@@ -253,6 +254,7 @@ setMethod(
 #' @examples
 #'
 #' library(MsFeatures)
+#' library(MsExperiment)
 #' ## Load a test data set with detected peaks
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
@@ -788,6 +790,7 @@ plotFeatureGroups <- function(x, xlim = numeric(), ylim = numeric(),
 #' @examples
 #'
 #' library(MsFeatures)
+#' library(MsExperiment)
 #' ## Load a test data set with detected peaks
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
diff --git a/R/methods-xcmsSet.R b/R/methods-xcmsSet.R
index 91b5a3c51..f2cb04913 100644
--- a/R/methods-xcmsSet.R
+++ b/R/methods-xcmsSet.R
@@ -1556,6 +1556,9 @@ setMethod("diffreport", "xcmsSet", function(object,
                                             h = 480, w = 640, mzdec=2,
                                             missing = numeric(), ...) {
 
+    if (!requireNamespace("multtest", quietly = TRUE))
+        stop("The use of 'diffreport' requires package 'multtest'. Please ",
+             "install with 'BiocInstaller::install(\"multtest\")'")
     if ( nrow(object@groups)<1 || length(object@groupidx) <1) {
         stop("No group information. Use group().")
     }
diff --git a/R/writemztab.R b/R/writemztab.R
index 873ba10dd..8aa294b9d 100644
--- a/R/writemztab.R
+++ b/R/writemztab.R
@@ -10,15 +10,15 @@
 ## utility function, combining different length objects into a dataframe
 ## padding short columns with NA
 rbind.ragged <- function(x, y) {
-    x <- as.data.frame(x) 
-    y <- as.data.frame(y) 
+    x <- as.data.frame(x)
+    y <- as.data.frame(y)
     colnames(x) <- seq(1:ncol(x))
     colnames(y) <- seq(1:ncol(y))
-    rbind.fill(x,y)
+    suppressWarnings(rbindFill(x,y))
 }
 
 cvTerm <- function(CV, accession, name, value) {
-    paste("[", paste(CV, accession, name, value, sep=", "), "]", sep="")    
+    paste("[", paste(CV, accession, name, value, sep=", "), "]", sep="")
 }
 #cvTerm("MS", "MS:1000443", "Mass Analyzer Type", "Orbitrap")
 
@@ -52,9 +52,9 @@ mzTabHeader <- function(mztab, version, mode, type, description, xset) {
 
     samples <- paste("sample[", 1:length(runs), "]", sep="")
     names(samples) <- paste("assay[", 1:length(runs), "]-sample_ref", sep="")
-    
+
     sampleDesc <- sampnames(xset)
-    names(sampleDesc) <- paste("sample[", 1:length(runs), "]-description", sep="")    
+    names(sampleDesc) <- paste("sample[", 1:length(runs), "]-description", sep="")
     filetypes <- mzFileType(runs)
     names(runs) <- paste("ms_run[", 1:length(filetypes), "]-format", sep="")
 
@@ -64,10 +64,10 @@ mzTabHeader <- function(mztab, version, mode, type, description, xset) {
     variableAssays <- unlist(tapply(seq(along=sampclass(xset)), sampclass(xset), function(x)
                                     paste(paste("assay[",x,"]", sep=""), collapse=",")))
     names(variableAssays) <- paste("study_variable[", seq(along=variableAssays), "]-assay_refs", sep="")
-    
+
     variableDescriptions <- unique(as.character(sampclass(xset)))
     names(variableDescriptions) <- paste("study_variable[", seq(along=variableDescriptions), "]-description", sep="")
-    
+
     mztab <- rbind.ragged(mztab, mzTabAddComment("Meta data section"))
     mztab <- rbind.ragged(mztab, mzTabAddTagValue("MTD",
                                                   c("mzTab-version"=version,
@@ -78,7 +78,7 @@ mzTabHeader <- function(mztab, version, mode, type, description, xset) {
 
     mztab <- rbind.ragged(mztab, mzTabAddTagValue("MTD", samples))
     mztab <- rbind.ragged(mztab, mzTabAddTagValue("MTD", sampleDesc))
-    
+
     mztab <- rbind.ragged(mztab, mzTabAddTagValue("MTD", assays))
     mztab <- rbind.ragged(mztab, mzTabAddTagValue("MTD", variableAssays))
     mztab <- rbind.ragged(mztab, mzTabAddTagValue("MTD", variableDescriptions))
@@ -95,7 +95,7 @@ mzTabAddTagValue <- function(section, values) {
 mzTabAddValues <- function(mztab, headers, section, values) {
     h <- cbind.data.frame(headers, t(names(values)), stringsAsFactors=FALSE)
     v <- cbind.data.frame(section, values, stringsAsFactors=FALSE)
-    
+
     mztab <- rbind.ragged(mztab, h)
     mztab <- rbind.ragged(mztab, v)
 }
@@ -103,14 +103,14 @@ mzTabAddValues <- function(mztab, headers, section, values) {
 mzTabAddSME <- function(mztab, xset) {
     runs <- seq(along=sampnames(xset))
     variables <- seq(along=levels(sampclass(xset)))
-    
+
     idHeaders <- c("identifier", "description", "chemical_formula",
                    "smiles", "inchi_key", "database", "database_version")
 
     searchHeaders1 <- c("search_engine", "best_search_engine_score")
-   
+
     searchHeaders2 <- paste("search_engine_score_ms_run[", runs, "]", sep="")
-    
+
     searchHeaders3 <- c("reliability", "modifications")
 
     featureHeaders <- c("charge", "adduct_ion", "exp_mass_to_charge",
@@ -118,8 +118,8 @@ mzTabAddSME <- function(mztab, xset) {
                         "retention_time_window", "uri", "spectra_ref")
 
     abundanceAssayHeaders <- paste("smallmolecule_abundance_assay[", runs, "]", sep="")
-    
-    
+
+
     abundanceVariableHeaders <- unlist(lapply(variables, FUN=function(v) c(paste("smallmolecule_abundance_study_variable[", v,"]", sep=""),
                                   paste("smallmolecule_abundance_stddev_study_variable[", v,"]", sep=""),
                                   paste("smallmolecule_abundance_std_error_study_variable[", v,"]", sep=""))))
@@ -132,7 +132,7 @@ mzTabAddSME <- function(mztab, xset) {
 
     g <- groups(xset)
     v <- groupval(xset, value="into")
-    
+
     result <-  as.data.frame(matrix(character(0), ncol=length(headers), nrow=nrow(g)))
     colnames(result) <- headers
 
@@ -140,14 +140,14 @@ mzTabAddSME <- function(mztab, xset) {
     #variableAssays <- unlist(tapply(seq(along=sampclass(xset)), sampclass(xset), function(x)
     #                         paste(paste("assay[",x,"]", sep=""), collapse=",")))
     #names(variableAssays) <- paste("study_variable[", seq(along=variableAssays), "]-assay_refs", sep="")
-    
-    
+
+
     result[,"retention_time"] <- g[,"rtmed"]
     result[,"exp_mass_to_charge"] <- g[,"mzmed"]
     result[, grepl("smallmolecule_abundance_assay", colnames(result))] <- v
-    
+
     mztab <- mzTabAddValues(mztab, "SEH", "SME", result)
-    
+
 }
 
 writeMzTab <- function(object, filename) {
@@ -177,7 +177,7 @@ if (FALSE) {
                        xset=xs)
     mzt <- xcms:::mzTabAddSME(mzt, xs)
     ##mzt
-    
+
     xcms:::writeMzTab(mzt, "faahKO.mzTab")
 }
 
@@ -186,7 +186,3 @@ if (FALSE) {
     library(MSnbase)
     m <- readMzTabData("faahKO.mzTab")
 }
-
-
-
-       
diff --git a/data/faahko_sub.RData b/data/faahko_sub.RData
index f62256251..54490a1b0 100644
Binary files a/data/faahko_sub.RData and b/data/faahko_sub.RData differ
diff --git a/data/faahko_sub2.RData b/data/faahko_sub2.RData
index c58a21c5d..d7a9ffd61 100644
Binary files a/data/faahko_sub2.RData and b/data/faahko_sub2.RData differ
diff --git a/data/xdata.RData b/data/xdata.RData
index 4ba55713f..2cfa0b849 100644
Binary files a/data/xdata.RData and b/data/xdata.RData differ
diff --git a/data/xmse.RData b/data/xmse.RData
index 1e9a8b600..edbd17057 100644
Binary files a/data/xmse.RData and b/data/xmse.RData differ
diff --git a/inst/NEWS b/inst/NEWS
index 5e04e5189..a9df39024 100644
--- a/inst/NEWS
+++ b/inst/NEWS
@@ -1,4 +1,4 @@
-Changes in version 4.1.10
+Changes in version 4.1.12
 ----------------------
 
 - Implementation of the `LamaParama` class and method for the `adjustRtime()`
@@ -8,6 +8,17 @@ Changes in version 4.1.10
   `summarizeMatchLama()` and `plot(LamaParama)` which allows for evaluation of
   matching between lamas and chromPeaks.
 
+Changes in version 4.1.11
+----------------------
+
+- Clean up of required and suggested packages and namespace imports.
+
+Changes in version 4.1.10
+----------------------
+
+- Ensure backward compatibility for parameter objects that gained additional
+  slots.
+
 Changes in version 4.1.9
 ----------------------
 
diff --git a/man/XCMSnExp-class.Rd b/man/XCMSnExp-class.Rd
index 1753ee985..4dc7303ce 100644
--- a/man/XCMSnExp-class.Rd
+++ b/man/XCMSnExp-class.Rd
@@ -685,6 +685,7 @@ with feature definitions and phenodata information, into a
 \examples{
 
 ## Load a test data set with detected peaks
+library(MSnbase)
 data(faahko_sub)
 ## Update the path to the files for the local system
 dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
diff --git a/man/XCMSnExp-filter-methods.Rd b/man/XCMSnExp-filter-methods.Rd
index 98e14def3..ad854af25 100644
--- a/man/XCMSnExp-filter-methods.Rd
+++ b/man/XCMSnExp-filter-methods.Rd
@@ -191,6 +191,7 @@ the raw retention times with the adjusted ones.
 \examples{
 
 ## Loading a test data set with identified chromatographic peaks
+library(MSnbase)
 data(faahko_sub)
 ## Update the path to the files for the local system
 dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
diff --git a/man/XChromatogram.Rd b/man/XChromatogram.Rd
index 72703f9fe..8b2330810 100644
--- a/man/XChromatogram.Rd
+++ b/man/XChromatogram.Rd
@@ -600,6 +600,7 @@ being samples and rows features.
 ## ---- Creation of XChromatograms ----
 ##
 ## Create a XChromatograms from Chromatogram objects
+library(MSnbase)
 dta <- list(Chromatogram(rtime = 1:7, c(3, 4, 6, 12, 8, 3, 2)),
     Chromatogram(1:10, c(4, 6, 3, 4, 7, 13, 43, 34, 23, 9)))
 
@@ -689,6 +690,7 @@ plotChromPeakDensity(res, param = prm)
 res <- dropFeatureDefinitions(res)
 hasFeatures(res)
 
+library(MSnbase)
 ## Create a XChromatogram object
 pks <- matrix(nrow = 1, ncol = 6)
 colnames(pks) <- c("rt", "rtmin", "rtmax", "into", "maxo", "sn")
diff --git a/man/applyAdjustedRtime.Rd b/man/applyAdjustedRtime.Rd
index 1006c14ce..9b96133fa 100644
--- a/man/applyAdjustedRtime.Rd
+++ b/man/applyAdjustedRtime.Rd
@@ -34,6 +34,7 @@ history is preserved.
 \examples{
 
 ## Load a test data set with detected peaks
+library(MSnbase)
 data(faahko_sub)
 ## Update the path to the files for the local system
 dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
diff --git a/man/chromPeakChromatograms.Rd b/man/chromPeakChromatograms.Rd
index 276d96025..7fb8663dc 100644
--- a/man/chromPeakChromatograms.Rd
+++ b/man/chromPeakChromatograms.Rd
@@ -59,6 +59,9 @@ of length equal to the number of chromatographic peaks (and one column).
 \examples{
 
 ## Load a test data set with detected peaks
+library(MSnbase)
+library(xcms)
+library(MsExperiment)
 faahko_sub <- loadXcmsData("faahko_sub2")
 
 ## Get EICs for every detected chromatographic peak
diff --git a/man/chromatogram-method.Rd b/man/chromatogram-method.Rd
index 6522024c8..af488d48a 100644
--- a/man/chromatogram-method.Rd
+++ b/man/chromatogram-method.Rd
@@ -109,6 +109,7 @@ and use these (for the subsetting based on the provided parameter
 \examples{
 
 ## Load a test data set with identified chromatographic peaks
+library(MSnbase)
 data(faahko_sub)
 ## Update the path to the files for the local system
 dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
diff --git a/man/correlate-Chromatogram.Rd b/man/correlate-Chromatogram.Rd
index 0bd641072..d5eb143a2 100644
--- a/man/correlate-Chromatogram.Rd
+++ b/man/correlate-Chromatogram.Rd
@@ -81,6 +81,7 @@ correlation matrix might thus be different.
 }
 \examples{
 
+library(MSnbase)
 chr1 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
     intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))
 chr2 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
diff --git a/man/do_findChromPeaks_centWave.Rd b/man/do_findChromPeaks_centWave.Rd
index 9a91e2df9..4270e893d 100644
--- a/man/do_findChromPeaks_centWave.Rd
+++ b/man/do_findChromPeaks_centWave.Rd
@@ -219,7 +219,7 @@ res <- do_findChromPeaks_centWave(mz = unlist(mzs), int = unlist(ints),
 head(res)
 }
 \references{
-Ralf Tautenhahn, Christoph B\"{o}ttcher, and Steffen Neumann "Highly
+Ralf Tautenhahn, Christoph Böttcher, and Steffen Neumann "Highly
     sensitive feature detection for high resolution LC/MS"
     \emph{BMC Bioinformatics} 2008, 9:504
 }
diff --git a/man/do_findChromPeaks_massifquant.Rd b/man/do_findChromPeaks_massifquant.Rd
index 4c6e81951..d8f1cca69 100644
--- a/man/do_findChromPeaks_massifquant.Rd
+++ b/man/do_findChromPeaks_massifquant.Rd
@@ -155,7 +155,7 @@ Massifquant is a Kalman filter (KF)-based chromatographic peak
 }
 \details{
 This algorithm's performance has been tested rigorously
-    on high resolution LC/{OrbiTrap, TOF}-MS data in centroid mode.
+    on high resolution LC/(OrbiTrap, TOF)-MS data in centroid mode.
     Simultaneous kalman filters identify peaks and calculate their
     area under the curve. The default parameters are set to operate on
     a complex LC-MS Orbitrap sample. Users will find it useful to do some
diff --git a/man/do_groupChromPeaks_density.Rd b/man/do_groupChromPeaks_density.Rd
index 4b27d8a4e..739e915cb 100644
--- a/man/do_groupChromPeaks_density.Rd
+++ b/man/do_groupChromPeaks_density.Rd
@@ -109,6 +109,8 @@ accordingly.
 }
 \examples{
 ## Load the test file
+library(xcms)
+library(MsExperiment)
 faahko_sub <- loadXcmsData("faahko_sub2")
 
 ## Disable parallel processing for this example
diff --git a/man/extractMsData-method.Rd b/man/extractMsData-method.Rd
index a413ae3d7..7a1105412 100644
--- a/man/extractMsData-method.Rd
+++ b/man/extractMsData-method.Rd
@@ -55,6 +55,7 @@ data range if \code{rt} and \code{mz} are not defined).
 \examples{
 
 ## Load a test data set with detected peaks
+library(MSnbase)
 data(faahko_sub)
 ## Update the path to the files for the local system
 dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
diff --git a/man/featureChromatograms.Rd b/man/featureChromatograms.Rd
index 8d194e81b..725865883 100644
--- a/man/featureChromatograms.Rd
+++ b/man/featureChromatograms.Rd
@@ -163,6 +163,8 @@ is smaller if \code{x} contains also filled-in peaks (with \code{fillChromPeaks}
 \examples{
 
 ## Load a test data set with detected peaks
+library(xcms)
+library(MsExperiment)
 faahko_sub <- loadXcmsData("faahko_sub2")
 
 ## Disable parallel processing for this example
diff --git a/man/fillChromPeaks.Rd b/man/fillChromPeaks.Rd
index a57e33e05..25d671608 100644
--- a/man/fillChromPeaks.Rd
+++ b/man/fillChromPeaks.Rd
@@ -260,6 +260,8 @@ in the matrix returned by the \code{\link[=featureValues]{featureValues()}} meth
 \examples{
 
 ## Load a test data set with identified chromatographic peaks
+library(xcms)
+library(MsExperiment)
 res <- loadXcmsData("faahko_sub2")
 
 ## Disable parallel processing for this example
@@ -267,7 +269,7 @@ register(SerialParam())
 
 ## Perform the correspondence. We assign all samples to the same group.
 res <- groupChromPeaks(res,
-    param = PeakDensityParam(sampleGroups = rep(1, length(fileNames(res)))))
+    param = PeakDensityParam(sampleGroups = rep(1, length(res))))
 
 ## For how many features do we lack an integrated peak signal?
 sum(is.na(featureValues(res)))
diff --git a/man/filter-MChromatograms.Rd b/man/filter-MChromatograms.Rd
index ca96dfa68..2a8fea2d3 100644
--- a/man/filter-MChromatograms.Rd
+++ b/man/filter-MChromatograms.Rd
@@ -112,6 +112,7 @@ columns by column \code{sortBy = "maxo"} or \code{sortBy = "into"} of the
 }
 \examples{
 
+library(MSnbase)
 chr1 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
     intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))
 chr2 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
diff --git a/man/findChromPeaks-Chromatogram-CentWaveParam.Rd b/man/findChromPeaks-Chromatogram-CentWaveParam.Rd
index d7d5c2be7..9f342440b 100644
--- a/man/findChromPeaks-Chromatogram-CentWaveParam.Rd
+++ b/man/findChromPeaks-Chromatogram-CentWaveParam.Rd
@@ -47,6 +47,7 @@ detection artifacts.
 }
 \examples{
 
+library(MSnbase)
 ## Loading a test data set with identified chromatographic peaks
 faahko_sub <- loadXcmsData("faahko_sub2")
 faahko_sub <- filterRt(faahko_sub, c(2500, 3700))
@@ -64,11 +65,14 @@ xchr
 ## Plot data and identified peaks.
 plot(xchr)
 
+library(MsExperiment)
+library(xcms)
 ## Perform peak detection on an MChromatograms object
-od3 <- readMSData(c(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
+
+fls <- c(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
     system.file("cdf/KO/ko16.CDF", package = "faahKO"),
-    system.file("cdf/KO/ko18.CDF", package = "faahKO")),
-    mode = "onDisk")
+    system.file("cdf/KO/ko18.CDF", package = "faahKO"))
+od3 <- readMsExperiment(fls)
 
 ## Disable parallel processing for this example
 register(SerialParam())
diff --git a/man/findChromPeaks-centWave.Rd b/man/findChromPeaks-centWave.Rd
index f7f2ac351..ec5ac694f 100644
--- a/man/findChromPeaks-centWave.Rd
+++ b/man/findChromPeaks-centWave.Rd
@@ -59,6 +59,7 @@
 \alias{roiScales}
 \alias{roiScales<-,CentWaveParam-method}
 \alias{roiScales<-}
+\alias{as.list,CentWaveParam-method}
 \title{Chromatographic peak detection using the centWave method}
 \usage{
 CentWaveParam(
@@ -139,6 +140,8 @@ CentWaveParam(
 \S4method{roiScales}{CentWaveParam}(object)
 
 \S4method{roiScales}{CentWaveParam}(object) <- value
+
+\S4method{as.list}{CentWaveParam}(x, ...)
 }
 \arguments{
 \item{ppm}{\code{numeric(1)} defining the maximal tolerated m/z deviation in
@@ -249,6 +252,8 @@ detection should be performed. Defaults to \code{msLevel = 1}.}
 \item{value}{The value for the slot.}
 
 \item{f}{For \code{integrate}: a \code{CentWaveParam} object.}
+
+\item{x}{The parameter object.}
 }
 \value{
 The \code{CentWaveParam} function returns a \code{CentWaveParam}
@@ -366,20 +371,21 @@ snthresh(cwp) <- 25
 cwp
 
 ## Perform the peak detection using centWave on some of the files from the
-## faahKO package. Files are read using the readMSData from the MSnbase
-## package
+## faahKO package. Files are read using the `readMsExperiment` function
+## from the MsExperiment package
 library(faahKO)
 library(xcms)
+library(MsExperiment)
 fls <- dir(system.file("cdf/KO", package = "faahKO"), recursive = TRUE,
            full.names = TRUE)
-raw_data <- readMSData(fls[1], mode = "onDisk")
+raw_data <- readMsExperiment(fls[1])
 
 ## Perform the peak detection using the settings defined above.
 res <- findChromPeaks(raw_data, param = cwp)
 head(chromPeaks(res))
 }
 \references{
-Ralf Tautenhahn, Christoph B\"{o}ttcher, and Steffen Neumann "Highly
+Ralf Tautenhahn, Christoph Böttcher, and Steffen Neumann "Highly
 sensitive feature detection for high resolution LC/MS" \emph{BMC Bioinformatics}
 2008, 9:504
 }
diff --git a/man/findChromPeaks-massifquant.Rd b/man/findChromPeaks-massifquant.Rd
index 06fb4ec13..385101e3f 100644
--- a/man/findChromPeaks-massifquant.Rd
+++ b/man/findChromPeaks-massifquant.Rd
@@ -338,7 +338,7 @@ The \code{findChromPeaks,OnDiskMSnExp,MassifquantParam}
 }
 \details{
 This algorithm's performance has been tested rigorously
-    on high resolution LC/{OrbiTrap, TOF}-MS data in centroid mode.
+    on high resolution LC/(OrbiTrap, TOF)-MS data in centroid mode.
     Simultaneous kalman filters identify chromatographic peaks and calculate
     their area under the curve. The default parameters are set to operate on
     a complex LC-MS Orbitrap sample. Users will find it useful to do some
diff --git a/man/findPeaks-MSW.Rd b/man/findPeaks-MSW.Rd
index d09f6d041..9569fdd00 100644
--- a/man/findPeaks-MSW.Rd
+++ b/man/findPeaks-MSW.Rd
@@ -273,6 +273,7 @@ These methods and classes are part of the updated and modernized
 }
 \examples{
 
+library(MSnbase)
 ## Create a MSWParam object
 mp <- MSWParam()
 ## Change snthresh parameter
diff --git a/man/findPeaks.addPredictedIsotopeFeatures-methods.Rd b/man/findPeaks.addPredictedIsotopeFeatures-methods.Rd
index cb03ebefc..5ea4877bc 100644
--- a/man/findPeaks.addPredictedIsotopeFeatures-methods.Rd
+++ b/man/findPeaks.addPredictedIsotopeFeatures-methods.Rd
@@ -108,7 +108,7 @@
 \author{Ralf Tautenhahn}
 \encoding{UTF-8}
 \references{
-  Ralf Tautenhahn, Christoph B\"{o}ttcher, and Steffen Neumann
+  Ralf Tautenhahn, Christoph Böttcher, and Steffen Neumann
   "Highly sensitive feature detection for high resolution LC/MS"
   BMC Bioinformatics 2008, 9:504\\
   Hendrik Treutler and Steffen Neumann.
diff --git a/man/findPeaks.centWave-methods.Rd b/man/findPeaks.centWave-methods.Rd
index d1734d2bd..811b4beec 100644
--- a/man/findPeaks.centWave-methods.Rd
+++ b/man/findPeaks.centWave-methods.Rd
@@ -120,7 +120,7 @@
 \author{Ralf Tautenhahn}
 \encoding{UTF-8}
 \references{
-  Ralf Tautenhahn, Christoph B\"{o}ttcher, and Steffen Neumann
+  Ralf Tautenhahn, Christoph Böttcher, and Steffen Neumann
   "Highly sensitive feature detection for high resolution LC/MS"
   BMC Bioinformatics 2008, 9:504
 }
diff --git a/man/findPeaks.centWaveWithPredictedIsotopeROIs-methods.Rd b/man/findPeaks.centWaveWithPredictedIsotopeROIs-methods.Rd
index ed8cd0cf0..f2baba7ea 100644
--- a/man/findPeaks.centWaveWithPredictedIsotopeROIs-methods.Rd
+++ b/man/findPeaks.centWaveWithPredictedIsotopeROIs-methods.Rd
@@ -125,7 +125,7 @@
 \author{Ralf Tautenhahn}
 \encoding{UTF-8}
 \references{
-  Ralf Tautenhahn, Christoph B\"{o}ttcher, and Steffen Neumann
+  Ralf Tautenhahn, Christoph Böttcher, and Steffen Neumann
   "Highly sensitive feature detection for high resolution LC/MS"
   BMC Bioinformatics 2008, 9:504\\
   Hendrik Treutler and Steffen Neumann.
diff --git a/man/groupChromPeaks.Rd b/man/groupChromPeaks.Rd
index fe6dbdaff..5a4049523 100644
--- a/man/groupChromPeaks.Rd
+++ b/man/groupChromPeaks.Rd
@@ -61,6 +61,7 @@
 \alias{kNN}
 \alias{kNN<-,NearestPeaksParam-method}
 \alias{kNN<-}
+\alias{as.list,PeakDensityParam-method}
 \alias{groupChromPeaks,XCMSnExp,PeakDensityParam-method}
 \alias{groupChromPeaks,XCMSnExp,MzClustParam-method}
 \alias{groupChromPeaks,XCMSnExp,NearestPeaksParam-method}
@@ -162,6 +163,8 @@ NearestPeaksParam(
 
 \S4method{kNN}{NearestPeaksParam}(object) <- value
 
+\S4method{as.list}{PeakDensityParam}(x, ...)
+
 \S4method{groupChromPeaks}{XCMSnExp,PeakDensityParam}(object, param, msLevel = 1L, add = FALSE)
 
 \S4method{groupChromPeaks}{XCMSnExp,MzClustParam}(object, param, msLevel = 1L)
@@ -236,6 +239,8 @@ distance for retention times.}
 nearest neighbors to check.}
 
 \item{value}{The value for the slot.}
+
+\item{x}{The parameter object.}
 }
 \value{
 For \code{groupChromPeaks}: either an \code{\link[=XcmsExperiment]{XcmsExperiment()}} or \code{\link[=XCMSnExp]{XCMSnExp()}}
diff --git a/man/groupFeatures-abundance-correlation.Rd b/man/groupFeatures-abundance-correlation.Rd
index 27f139ba4..84477fa4a 100644
--- a/man/groupFeatures-abundance-correlation.Rd
+++ b/man/groupFeatures-abundance-correlation.Rd
@@ -62,6 +62,7 @@ parameters for the similarity calculation is available in the
 \examples{
 
 library(MsFeatures)
+library(MsExperiment)
 ## Load a test data set with detected peaks
 faahko_sub <- loadXcmsData("faahko_sub2")
 
diff --git a/man/groupFeatures-eic-similarity.Rd b/man/groupFeatures-eic-similarity.Rd
index 544b2a6ac..c3ceb206d 100644
--- a/man/groupFeatures-eic-similarity.Rd
+++ b/man/groupFeatures-eic-similarity.Rd
@@ -144,6 +144,7 @@ is excluded from the correlation.
 \examples{
 
 library(MsFeatures)
+library(MsExperiment)
 ## Load a test data set with detected peaks
 faahko_sub <- loadXcmsData("faahko_sub2")
 
diff --git a/man/groupFeatures-similar-rtime.Rd b/man/groupFeatures-similar-rtime.Rd
index 938f09ceb..0d56170ea 100644
--- a/man/groupFeatures-similar-rtime.Rd
+++ b/man/groupFeatures-similar-rtime.Rd
@@ -36,6 +36,7 @@ See \code{\link[MsFeatures:groupFeatures-similar-rtime]{MsFeatures::SimilarRtime
 \examples{
 
 library(MsFeatures)
+library(MsExperiment)
 ## Load a test data set with detected peaks
 faahko_sub <- loadXcmsData("faahko_sub2")
 
diff --git a/man/highlightChromPeaks.Rd b/man/highlightChromPeaks.Rd
index 14f83995e..e5e46fb90 100644
--- a/man/highlightChromPeaks.Rd
+++ b/man/highlightChromPeaks.Rd
@@ -73,6 +73,7 @@ peak definitions to an existing plot, such as one created by the
 \examples{
 
 ## Load a test data set with detected peaks
+library(MSnbase)
 data(faahko_sub)
 ## Update the path to the files for the local system
 dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
diff --git a/man/imputeRowMin.Rd b/man/imputeRowMin.Rd
index ec9effea9..b3999e3e6 100644
--- a/man/imputeRowMin.Rd
+++ b/man/imputeRowMin.Rd
@@ -20,6 +20,7 @@ with a proportion of the minimal value for that row (i.e.
 }
 \examples{
 
+library(MSnbase)
 library(faahKO)
 data("faahko")
 
diff --git a/man/imputeRowMinRand.Rd b/man/imputeRowMinRand.Rd
index f2d7368b5..147aebea4 100644
--- a/man/imputeRowMinRand.Rd
+++ b/man/imputeRowMinRand.Rd
@@ -66,6 +66,7 @@ fractions of the row minimum.
 \examples{
 
 library(faahKO)
+library(MSnbase)
 data("faahko")
 
 xset <- group(faahko)
diff --git a/man/overlappingFeatures.Rd b/man/overlappingFeatures.Rd
index ae10651c2..8bb937510 100644
--- a/man/overlappingFeatures.Rd
+++ b/man/overlappingFeatures.Rd
@@ -35,6 +35,7 @@ the m/z - rt space.
 \examples{
 
 ## Load a test data set with detected peaks
+library(MSnbase)
 data(faahko_sub)
 ## Update the path to the files for the local system
 dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
diff --git a/man/peaksWithCentWave.Rd b/man/peaksWithCentWave.Rd
index fc78b8dba..189b6c22c 100644
--- a/man/peaksWithCentWave.Rd
+++ b/man/peaksWithCentWave.Rd
@@ -107,9 +107,9 @@ resulting in different signal to noise ratios.
 \examples{
 
 ## Reading a file
+library(MsExperiment)
 library(xcms)
-od <- readMSData(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
-    mode = "onDisk")
+od <- readMsExperiment(system.file("cdf/KO/ko15.CDF", package = "faahKO"))
 
 ## Extract chromatographic data for a small m/z range
 mzr <- c(272.1, 272.2)
diff --git a/man/plotChromPeakDensity.Rd b/man/plotChromPeakDensity.Rd
index b4726caf6..db48c5fdf 100644
--- a/man/plotChromPeakDensity.Rd
+++ b/man/plotChromPeakDensity.Rd
@@ -98,6 +98,7 @@ algorithm and its supported settings.
 \examples{
 
 ## Load a test data set with detected peaks
+library(MSnbase)
 data(faahko_sub)
 ## Update the path to the files for the local system
 dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
diff --git a/man/plotChromatogramsOverlay.Rd b/man/plotChromatogramsOverlay.Rd
index f558d4cb2..1030ad61d 100644
--- a/man/plotChromatogramsOverlay.Rd
+++ b/man/plotChromatogramsOverlay.Rd
@@ -116,6 +116,7 @@ the \code{plot} function for \code{XChromatogram()} object for details).
 
 ## Load preprocessed data and extract EICs for some features.
 library(xcms)
+library(MSnbase)
 xdata <- loadXcmsData()
 data(xdata)
 ## Update the path to the files for the local system
diff --git a/man/plotMsData.Rd b/man/plotMsData.Rd
index 075398458..ad6f1a55b 100644
--- a/man/plotMsData.Rd
+++ b/man/plotMsData.Rd
@@ -35,27 +35,14 @@ based on their intensity. See argument \code{col.regions} in
 \link[lattice:level.colors]{lattice::level.colors} documentation.}
 }
 \description{
-\strong{UPDATE}: please use \code{plot(x, type = "XIC")} from the \code{MSnbase} package
-instead. See examples below.
+\strong{UPDATE}: please use \code{plot()} from the \code{MsExperiment} or
+\code{plot(x, type = "XIC")} from the \code{MSnbase} package instead. See examples
+in the vignette for more information.
 
 The \code{plotMsData} creates a plot that combines an (base peak )
 extracted ion chromatogram on top (rt against intensity) and a plot of
 rt against m/z values at the bottom.
 }
-\examples{
-
-## Read two files from the faahKO package
-library(faahKO)
-cdfs <- dir(system.file("cdf", package = "faahKO"), full.names = TRUE,
-    recursive = TRUE)[1:2]
-raw_data <- readMSData(cdfs, mode = "onDisk")
-
-## Subset the object to a rt and mz range and plot the data.
-raw_data |>
-    filterRt(rt = c(2700, 2900)) |>
-    filterMz(mz = c(334.9, 335.1)) |>
-    plot(type = "XIC")
-}
 \author{
 Johannes Rainer
 }
diff --git a/man/refineChromPeaks.Rd b/man/refineChromPeaks.Rd
index d23bdeccb..b1472702b 100644
--- a/man/refineChromPeaks.Rd
+++ b/man/refineChromPeaks.Rd
@@ -203,6 +203,8 @@ calculation of the peak signal (\code{"into"}).
 \examples{
 
 ## Load a test data set with detected peaks
+library(xcms)
+library(MsExperiment)
 faahko_sub <- loadXcmsData("faahko_sub2")
 
 ## Disable parallel processing for this example
diff --git a/man/removeIntensity-Chromatogram.Rd b/man/removeIntensity-Chromatogram.Rd
index 18cc89a16..5343689a6 100644
--- a/man/removeIntensity-Chromatogram.Rd
+++ b/man/removeIntensity-Chromatogram.Rd
@@ -52,6 +52,7 @@ chromatographic data.
 }
 \examples{
 
+library(MSnbase)
 chr <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
     intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))
 
diff --git a/man/storeResults.Rd b/man/storeResults.Rd
index a72a4c8cd..e943c9932 100644
--- a/man/storeResults.Rd
+++ b/man/storeResults.Rd
@@ -36,6 +36,8 @@ listed above.
 \examples{
 
 ## Load a test data set with detected peaks
+library(xcms)
+library(MsExperiment)
 faahko_sub <- loadXcmsData("faahko_sub2")
 
 ## Set up parameter to save as .RData file
diff --git a/tests/testthat.R b/tests/testthat.R
index 71624c6d0..cf8ea5a2d 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,6 +1,7 @@
 library(testthat)
 library(xcms)
 library(faahKO)
+library(MSnbase)
 library(msdata)
 
 if (.Platform$OS.type == "unix") {
diff --git a/vignettes/LC-MS-feature-grouping.Rmd b/vignettes/LC-MS-feature-grouping.Rmd
index bac3e990d..5269f33c4 100644
--- a/vignettes/LC-MS-feature-grouping.Rmd
+++ b/vignettes/LC-MS-feature-grouping.Rmd
@@ -67,6 +67,7 @@ result from this pre-processing updating also the location of the respective raw
 data files on the current machine.
 
 ```{r load-data}
+library(MSnbase)
 library(xcms)
 library(faahKO)
 library(MsFeatures)
diff --git a/vignettes/xcms-direct-injection.Rmd b/vignettes/xcms-direct-injection.Rmd
index 3a5868944..ed496adce 100644
--- a/vignettes/xcms-direct-injection.Rmd
+++ b/vignettes/xcms-direct-injection.Rmd
@@ -12,7 +12,7 @@ vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteKeywords{Mass Spectrometry, MS, Metabolomics, Bioinformatics}
   %\VignetteEncoding{UTF-8}
-  %\VignetteDepends{xcms,msdata,MassSpecWavelet,BiocStyle,signal}
+  %\VignetteDepends{xcms,msdata,MassSpecWavelet,BiocStyle,signal,MSnbase}
 ---
 
 ```{r style, echo = FALSE, results = 'asis'}
@@ -41,6 +41,7 @@ Below we load the required packages. For information on the parallel processing
 setup please see the *BiocParallel* vignette.
 
 ```{r load-libs, message = FALSE, results = "hide"}
+library(MSnbase)
 library(xcms)
 library(MassSpecWavelet)
 
diff --git a/xcms.Rproj b/xcms.Rproj
deleted file mode 100644
index 21a4da087..000000000
--- a/xcms.Rproj
+++ /dev/null
@@ -1,17 +0,0 @@
-Version: 1.0
-
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source