fix: avoid error message from issue #584

- Add ... to findChromPeaks,OnDiskMSnExp to avoid error message from issue #584.
sneumann · Nov 3, 2021 · 062a48a · 062a48a
1 parent 6db8f84
commit 062a48a
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Showing 9 changed files with 34 additions and 15 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.1', bioc: 'devel'}
-          - { os: windows-latest, r: '4.1', bioc: 'devel'}
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.15', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.15'}
+          - { os: windows-latest, r: 'devel', bioc: '3.15'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 3.17.0
+Version: 3.17.1
 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,

diff --git a/R/methods-OnDiskMSnExp.R b/R/methods-OnDiskMSnExp.R
@@ -44,6 +44,8 @@
 #' @param msLevel \code{integer(1)} defining the MS level on which the peak
 #'     detection should be performed. Defaults to \code{msLevel = 1}.
 #'
+#' @param ... ignored.
+#'
 #' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
 #'     \code{\link{XCMSnExp}} object with the results of the peak detection.
 #'     If \code{return.type = "list"} a list of length equal to the number of
@@ -58,7 +60,7 @@
 setMethod("findChromPeaks",
           signature(object = "OnDiskMSnExp", param = "CentWaveParam"),
           function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
-                   msLevel = 1L) {
+                   msLevel = 1L, ...) {
               return.type <- match.arg(return.type, c("XCMSnExp", "list",
                                                       "xcmsSet"))
               startDate <- date()
@@ -137,7 +139,7 @@ setMethod("findChromPeaks",
 setMethod("findChromPeaks",
           signature(object = "OnDiskMSnExp", param = "MatchedFilterParam"),
           function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
-                   msLevel = 1L) {
+                   msLevel = 1L, ...) {
               return.type <- match.arg(return.type, c("XCMSnExp", "list",
                                                       "xcmsSet"))
               startDate <- date()
@@ -230,7 +232,7 @@ setMethod("findChromPeaks",
 setMethod("findChromPeaks",
           signature(object = "OnDiskMSnExp", param = "MassifquantParam"),
           function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
-                   msLevel = 1L) {
+                   msLevel = 1L, ...) {
               return.type <- match.arg(return.type, c("XCMSnExp", "list",
                                                       "xcmsSet"))
               startDate <- date()
@@ -299,7 +301,7 @@ setMethod("findChromPeaks",
 setMethod("findChromPeaks",
           signature(object = "OnDiskMSnExp", param = "MSWParam"),
           function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
-                   msLevel = 1L) {
+                   msLevel = 1L, ...) {
               return.type <- match.arg(return.type, c("XCMSnExp", "list",
                                                       "xcmsSet"))
               startDate <- date()
@@ -370,7 +372,7 @@ setMethod("findChromPeaks",
 setMethod("findChromPeaks",
           signature(object = "OnDiskMSnExp", param = "CentWavePredIsoParam"),
           function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
-                   msLevel = 1L) {
+                   msLevel = 1L, ...) {
               return.type <- match.arg(return.type, c("XCMSnExp", "list",
                                                       "xcmsSet"))
               startDate <- date()

diff --git a/inst/NEWS b/inst/NEWS
@@ -1,7 +1,11 @@
+Changes in version 3.17.1
+
+- Fix error message from issue [584](https://github.com/sneumann/xcms/issues/584).
+
 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  
+- Disable parallel processing on Windows, causing an issue in testthat on BioC build check
 
 Changes in version 3.15.4
 

diff --git a/man/findChromPeaks-centWave.Rd b/man/findChromPeaks-centWave.Rd
diff --git a/man/findChromPeaks-centWaveWithPredIsoROIs.Rd b/man/findChromPeaks-centWaveWithPredIsoROIs.Rd
diff --git a/man/findChromPeaks-massifquant.Rd b/man/findChromPeaks-massifquant.Rd
diff --git a/man/findChromPeaks-matchedFilter.Rd b/man/findChromPeaks-matchedFilter.Rd
diff --git a/man/findPeaks-MSW.Rd b/man/findPeaks-MSW.Rd