revert main merge

.Rbuildignore

@@ -1,7 +1,6 @@
 ^\.github$
 .editorconfig
 .travis.yml
-man/figures*
 local_data
 favicon
 logo.png

.editorconfig

@@ -6,7 +6,7 @@ root = true
 charset = utf-8
 end_of_line = lf
 trim_trailing_whitespace = true
-insert_final_newline = true
+insert_final_newline = false
 
 [*.R]
 indent_style = space
@@ -22,4 +22,4 @@ indent_style = tab
 
 [*.yml]
 indent_style = space
-indent_size = 2
+indent_size = 2

.github/workflows/check-bioc.yml

@@ -22,8 +22,7 @@
 
 on:
   push:
-    paths-ignore:
-      - 'README.md'
+  pull_request:
 
 name: R-CMD-check-bioc
 
@@ -53,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
-          - { os: windows-latest, r: '4.4', bioc: '3.20'}
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: 'next', bioc: '3.19'}
+          - { os: windows-latest, r: 'next', bioc: '3.19'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -126,7 +125,32 @@ jobs:
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
         run: |
-        shell: Rscript {0}
+          ## Enable installing XML from source if needed
+          brew install libxml2
+          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
+
+          ## Required to install magick as noted at
+          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
+          brew install imagemagick@6
+
+          ## For textshaping, required by ragg, and required by pkgdown
+          brew install harfbuzz fribidi
+
+          brew install libgit2
+          ## Helps compile RCurl from source
+          ## brew uninstall curl
+
+          ## required for ncdf4 - can not use the homebrew one because that uses GCC
+          ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/
+          curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz
+          tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C /
+          rm netcdf-4.7.4-darwin.17-x86_64.tar.gz
+          curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz
+          tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C /
+          rm hdf5-1.12.0-darwin.17-x86_64.tar.gz
+          curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz
+          tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C /
+          rm szip-2.1.1-darwin.17-x86_64.tar.gz
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
@@ -239,7 +263,7 @@ jobs:
       - name: Test coverage
         if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
-          covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
+          covr::codecov()
         shell: Rscript {0}
 
       - name: Install package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.17.2
+Version: 1.15.0
 Description: The Spectra package defines an efficient infrastructure
    for storing and handling mass spectrometry spectra and functionality to
    subset, process, visualize and compare spectra data. It provides different
@@ -40,9 +40,9 @@ Authors@R: c(person(given = "RforMassSpectrometry Package Maintainer",
 Depends:
     R (>= 4.0.0),
     S4Vectors,
-    BiocParallel
+    BiocParallel,
+    ProtGenerics (>= 1.35.4)
 Imports:
-    ProtGenerics (>= 1.37.1),
     methods,
     IRanges,
     MsCoreUtils (>= 1.7.5),

NAMESPACE

@@ -8,7 +8,6 @@ export(MsBackendMemory)
 export(MsBackendMzR)
 export(PrecursorMzParam)
 export(applyProcessing)
-export(asDataFrame)
 export(chunkapply)
 export(combinePeaksData)
 export(combineSpectra)
@@ -17,8 +16,8 @@ export(concatenateSpectra)
 export(coreSpectraVariables)
 export(countIdentifications)
 export(deisotopeSpectra)
+export(estimatePrecursorIntensity)
 export(estimatePrecursorMz)
-export(filterPeaksRanges)
 export(filterPrecursorIsotopes)
 export(filterPrecursorMaxIntensity)
 export(filterPrecursorPeaks)
@@ -51,16 +50,13 @@ exportMethods("centroided<-")
 exportMethods("collisionEnergy<-")
 exportMethods("dataOrigin<-")
 exportMethods("dataStorage<-")
-exportMethods("dataStorageBasePath<-")
 exportMethods("intensity<-")
 exportMethods("isolationWindowLowerMz<-")
 exportMethods("isolationWindowTargetMz<-")
 exportMethods("isolationWindowUpperMz<-")
-exportMethods("msLevel<-")
 exportMethods("mz<-")
 exportMethods("peaksData<-")
 exportMethods("polarity<-")
-exportMethods("precursorMz<-")
 exportMethods("rtime<-")
 exportMethods("smoothed<-")
 exportMethods("spectraData<-")
@@ -72,7 +68,6 @@ exportMethods(backendBpparam)
 exportMethods(backendInitialize)
 exportMethods(backendMerge)
 exportMethods(backendParallelFactor)
-exportMethods(backendRequiredSpectraVariables)
 exportMethods(bin)
 exportMethods(c)
 exportMethods(cbind2)
@@ -84,12 +79,9 @@ exportMethods(containsMz)
 exportMethods(containsNeutralLoss)
 exportMethods(dataOrigin)
 exportMethods(dataStorage)
-exportMethods(dataStorageBasePath)
 exportMethods(dropNaSpectraVariables)
 exportMethods(entropy)
-exportMethods(estimatePrecursorIntensity)
 exportMethods(export)
-exportMethods(extractByIndex)
 exportMethods(filterAcquisitionNum)
 exportMethods(filterDataOrigin)
 exportMethods(filterDataStorage)
@@ -166,7 +158,6 @@ importFrom(MsCoreUtils,coefMA)
 importFrom(MsCoreUtils,coefSG)
 importFrom(MsCoreUtils,coefWMA)
 importFrom(MsCoreUtils,common)
-importFrom(MsCoreUtils,common_path)
 importFrom(MsCoreUtils,entropy)
 importFrom(MsCoreUtils,group)
 importFrom(MsCoreUtils,i2index)
@@ -210,7 +201,6 @@ importFrom(methods,.hasSlot)
 importFrom(methods,.valueClassTest)
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
-importFrom(methods,existsMethod)
 importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,setAs)
@@ -235,11 +225,9 @@ importMethodsFrom(ProtGenerics,"intensity<-")
 importMethodsFrom(ProtGenerics,"isolationWindowLowerMz<-")
 importMethodsFrom(ProtGenerics,"isolationWindowTargetMz<-")
 importMethodsFrom(ProtGenerics,"isolationWindowUpperMz<-")
-importMethodsFrom(ProtGenerics,"msLevel<-")
 importMethodsFrom(ProtGenerics,"mz<-")
 importMethodsFrom(ProtGenerics,"peaksData<-")
 importMethodsFrom(ProtGenerics,"polarity<-")
-importMethodsFrom(ProtGenerics,"precursorMz<-")
 importMethodsFrom(ProtGenerics,"rtime<-")
 importMethodsFrom(ProtGenerics,"smoothed<-")
 importMethodsFrom(ProtGenerics,"spectraData<-")
@@ -256,7 +244,6 @@ importMethodsFrom(ProtGenerics,collisionEnergy)
 importMethodsFrom(ProtGenerics,compareSpectra)
 importMethodsFrom(ProtGenerics,dataOrigin)
 importMethodsFrom(ProtGenerics,dataStorage)
-importMethodsFrom(ProtGenerics,estimatePrecursorIntensity)
 importMethodsFrom(ProtGenerics,filterAcquisitionNum)
 importMethodsFrom(ProtGenerics,filterDataOrigin)
 importMethodsFrom(ProtGenerics,filterDataStorage)

NEWS.md

@@ -1,80 +1,10 @@
-# Spectra 1.17
+# Spectra 1.15
 
-## Changes in 1.17.2
+## Changes in 1.15.0
 
 - Add `cbind2()` method to easily add multiple `spectraVariables` to the
   `spectraData`
 
-## Changes in 1.17.1
-
-- Refactor `containsMz()` to support chunk-wise processing.
-
-# Spectra 1.15
-
-## Changes in 1.15.13
-
-- Add `precursorMz<-` method [issue #336](https://github.com/rformassspectrometry/Spectra/issues/336).
-
-## Changes in 1.15.12
-
-- Add generic `backendRequiredSpectraVariables()` to allow definition of
-  mandatory spectra variables for a backend.
-
-## Changes in 1.15.11
-
-- Add reference to `MsBackendMetaboLights`.
-
-## Changes in 1.15.10
-
-- Add new `extractSpectra()` generic and implementation for `MsBackend`. Fixes
-  [issue #5](https://github.com/rformassspectrometry/MsBackendMetaboLights/issues/5).
-
-## Changes in 1.15.9
-
-- Restructure and reorganize documentation for `Spectra`.
-
-## Changes in 1.15.8
-
-- Refactor the `Spectra()` constructor method: better support for
-  initialization of backends that define their own specific parameters.
-
-## Changes in 1.15.7
-
-- Change `estimatePrecursorIntensity()` to a method to avoid overrides/clashes
-  with the same-named implementation in *xcms*.
-
-## Changes in 1.15.6
-
-- Fix in `selectSpectraVariables()` for `MsBackendMzR`: ensure peaks variables
-  `"mz"` and `"intensity"` are not by default removed.
-
-## Changes in 1.15.5
-
-- Add new `filterPeaksRanges()` function to filter mass peaks by ranges on
-  numeric spectra or peak variables.
-
-## Changes in 1.15.3
-
-- For evaluation of the `Spectra`'s processing queue: call functions from the
-  *MetaboCoreUtils* directly through their namespace (`MsCoreUtils::`) to avoid
-  errors if performed in parallel on Windows machines or if called on a
-  re-loaded object.
-- New `asDataFrame()` function to convert a (small) `Spectra` object
-  into a long `DataFrame`.
-
-## Changes in 1.15.2
-
-- Add `dataStorageDataPath()` and `dataStorageDataPath<-` methods to allow
-  updating/adapting the path of the data storage files of backends supporting
-  that [issue #321](https://github.com/rformassspectrometry/Spectra/issues/321).
-
-## Changes in 1.15.1
-
-- Improve documentation for `combineSpectra()` and `combinePeaks()` [issue
-  #320](https://github.com/rformassspectrometry/Spectra/issues/320).
-
-# Spectra 1.13
-
 ## Changes in 1.13.8
 
 - Add `estimatePrecursorMz()` function to *estimate* the precursor m/z for DDA

R/AllGenerics.R

@@ -1,40 +1,42 @@
 #' @include hidden_aliases.R
 NULL
 
-setGeneric("backendRequiredSpectraVariables", function(object, ...)
-          standardGeneric("backendRequiredSpectraVariables"))
 #' @rdname hidden_aliases
 setMethod("bin", "numeric", MsCoreUtils::bin)
 setGeneric("combinePeaks", function(object, ...)
            standardGeneric("combinePeaks"))
+#' @rdname hidden_aliases
 setGeneric("containsMz", function(object, ...)
     standardGeneric("containsMz"))
+#' @rdname hidden_aliases
 setGeneric("containsNeutralLoss", function(object, ...)
     standardGeneric("containsNeutralLoss"))
-setGeneric("dataStorageBasePath", function(object, ...)
-    standardGeneric("dataStorageBasePath"))
-setGeneric("dataStorageBasePath<-", function(object, ..., value)
-    standardGeneric("dataStorageBasePath<-"))
+#' @rdname hidden_aliases
 setGeneric("dropNaSpectraVariables", function(object, ...)
     standardGeneric("dropNaSpectraVariables"))
+#' @rdname hidden_aliases
 setGeneric("entropy", function(object, ...)
   standardGeneric("entropy"))
+#' @rdname hidden_aliases
 setGeneric("export", function(object, ...)
     standardGeneric("export"))
-setGeneric("extractByIndex", function(object, i)
-    standardGeneric("extractByIndex"))
 setGeneric("filterFourierTransformArtefacts", function(object, ...)
     standardGeneric("filterFourierTransformArtefacts"))
+#' @rdname neutralLoss
 setGeneric("neutralLoss", function(object, param, ...)
     standardGeneric("neutralLoss"))
+#' @rdname hidden_aliases
 setGeneric("pickPeaks", function(object, ...)
     standardGeneric("pickPeaks"))
 setGeneric("plotSpectraMirror", function(x, y, ...)
     standardGeneric("plotSpectraMirror"))
+#' @rdname hidden_aliases
 setGeneric("replaceIntensitiesBelow", function(object, threshold = min, ...)
     standardGeneric("replaceIntensitiesBelow"))
+#' @rdname hidden_aliases
 setGeneric("reset", function(object, ...)
     standardGeneric("reset"))
+#' @rdname hidden_aliases
 setGeneric("selectSpectraVariables", function(object, ...)
     standardGeneric("selectSpectraVariables"))
 setGeneric("Spectra", function(object, ...) standardGeneric("Spectra"))