merge

DESCRIPTION

@@ -13,6 +13,7 @@ Authors@R: c(person(given = "Christian",
       comment = c(ORCID = "0000-0003-0288-9619")))
 Depends: R (>= 4.1), methods, Spectra (>= 1.5.8)
 Imports:
+    ProtGenerics (>= 1.35.3),
     MsCoreUtils,
     S4Vectors,
     IRanges,
@@ -40,7 +41,7 @@ BugReports: https://github.com/fgcz/MsBackendRawFileReader/issues
 Encoding: UTF-8
 NeedsCompilation: yes
 biocViews: MassSpectrometry, Proteomics, Metabolomics
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1
 License: GPL-3
 SystemRequirements: mono-runtime 4.x or higher (including System.Data library)
     on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows.

INSTALL

@@ -3,3 +3,18 @@
 Please follow the install notes of the rawrr package.
 
 https://bioconductor.org/packages/rawrr/
+
+The `Dockerfile` performing `R CMD build` and `R CMD check` requires
+
+```
+from bioconductor/bioconductor_docker:devel
+run apt-get update && apt-get install mono-mcs mono-xbuild -y
+run apt-get install texlive-base texlive-latex-extra texinfo texlive-fonts-extra -y
+run R -q -e "BiocManager::install(c('BiocStyle', 'ExperimentHub', 'knitr', 'protViz', 'rmarkdown', 'tartare', 'testthat'))"
+run R -q -e "BiocManager::install(c('rawrr', 'ggplot2', 'hexbin', 'BiocParallel', 'reshape2', 'scales'))"
+run R -q -e "BiocManager::install(c('MsCoreUtils', 'S4Vectors', 'IRanges', 'utils', 'Spectra'))"
+run R -q -e "BiocManager::install(c('mzR', 'MsBackendMgf'))"
+```
+
+
+

NAMESPACE

@@ -7,12 +7,13 @@ exportMethods("[")
 exportMethods(filterScan)
 exportMethods(intensity)
 exportMethods(scanType)
-import(Spectra)
 importClassesFrom(IRanges,NumericList)
+importClassesFrom(Spectra,MsBackendDataFrame)
 importFrom(BiocParallel,bpparam)
 importFrom(IRanges,NumericList)
 importFrom(MsCoreUtils,i2index)
 importFrom(MsCoreUtils,rbindFill)
+importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,extractROWS)
 importFrom(methods,"slot<-")
 importFrom(methods,callNextMethod)
@@ -21,3 +22,7 @@ importFrom(rawrr,readIndex)
 importFrom(utils,packageVersion)
 importMethodsFrom(BiocParallel,bplapply)
 importMethodsFrom(BiocParallel,bpmapply)
+importMethodsFrom(ProtGenerics,backendInitialize)
+importMethodsFrom(ProtGenerics,dataStorage)
+importMethodsFrom(ProtGenerics,intensity)
+importMethodsFrom(ProtGenerics,peaksData)

R/MsBackendRawFileReader-functions.R

@@ -41,6 +41,8 @@ NULL
 )
 
 
+#' @importFrom S4Vectors DataFrame
+#' 
 .MsBackendRawFileReader_header <- function(x = character()) {
   if (length(x) != 1)
     stop("'x' should have length 1")
@@ -75,8 +77,8 @@ NULL
 
   ## Remove core spectra variables that contain only `NA`
   hdr <- S4Vectors::DataFrame(hdr[, !(MsCoreUtils::vapply1l(hdr, function(z) all(is.na(z))) &
-                                 colnames(hdr) %in%
-                                 names(.SPECTRA_DATA_COLUMNS))
+                                      colnames(hdr) %in%
+                                      names(.SPECTRA_DATA_COLUMNS))
   ])
   .post_process_header(hdr)
 }

R/MsBackendRawFileReader.R

@@ -16,7 +16,9 @@ NULL
 #' 
 #'
 #' @author Christian Panse (2019-2021)
-#' @import Spectra
+#' 
+#' @importClassesFrom Spectra MsBackendDataFrame
+#' 
 #' @examples 
 #' beRaw <- Spectra::backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(),
 #'   files = rawrr::sampleFilePath())
@@ -44,6 +46,8 @@ setValidity("MsBackendRawFileReader", function(object) {
 #'
 #' @importMethodsFrom BiocParallel bpmapply bplapply
 #'
+#' @importMethodsFrom ProtGenerics backendInitialize
+#' 
 #' @importFrom BiocParallel bpparam 
 #' @importFrom rawrr readIndex
 setMethod("backendInitialize", "MsBackendRawFileReader",
@@ -85,6 +89,10 @@ setMethod("show", "MsBackendRawFileReader", function(object) {
 })
 
 #' @rdname hidden_aliases
+#'
+#' @importMethodsFrom ProtGenerics peaksData
+#'
+#' @importMethodsFrom ProtGenerics dataStorage
 setMethod("peaksData", "MsBackendRawFileReader",
           function(object, ..., BPPARAM = bpparam()) {
             if (!length(object))
@@ -140,6 +148,7 @@ setMethod("[", "MsBackendRawFileReader", function(x, i, j, ..., drop = FALSE) {
 
 #' @importClassesFrom IRanges NumericList
 #' @rdname hidden_aliases
+#' @importMethodsFrom ProtGenerics intensity
 #' @exportMethod intensity
 setMethod("intensity", "MsBackendRawFileReader", function(object, ..., BPPARAM = bpparam()) {
   IRanges::NumericList(lapply(peaksData(object, BPPARAM = BPPARAM), "[", , 2), compress = FALSE)