diff --git a/DESCRIPTION b/DESCRIPTION index 7bc861a8..1d327e5d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: MSnbase Title: Base Functions and Classes for Mass Spectrometry and Proteomics -Version: 2.33.4 +Version: 2.33.5 Description: MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and @@ -194,7 +194,6 @@ Collate: 'methods-Spectrum2.R' 'methods-all.equal.R' 'methods-filters.R' - 'methods-fragments.R' 'methods-mzR.R' 'methods-other.R' 'methods-pSet.R' @@ -221,4 +220,4 @@ Collate: 'utils.R' 'writeMSData.R' 'zzz.R' -RoxygenNote: 7.2.3 \ No newline at end of file +RoxygenNote: 7.3.2 diff --git a/NEWS.md b/NEWS.md index 3c92c99f..24ab3a98 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # MSnbase 2.33 +## MSnbase 2.33.5 + +- Remove `methods-fragments.R` (is now part of `PSMatch`). + ## MSnbase 2.33.4 - Fix bug in `MzTab()` (see issue #608). diff --git a/R/methods-fragments.R b/R/methods-fragments.R deleted file mode 100644 index 542ccde4..00000000 --- a/R/methods-fragments.R +++ /dev/null @@ -1,10 +0,0 @@ -setMethod("calculateFragments", c("character", "missing"), - function(sequence, type = c("b", "y"), z = 1, - modifications = c(C = 57.02146), - neutralLoss = defaultNeutralLoss(), - verbose = isMSnbaseVerbose()) { - l <- lapply(sequence, PSMatch:::.calculateFragments, - type = type, z = z, modifications = modifications, - neutralLoss = neutralLoss, verbose = verbose) - return(do.call(rbind, l)) - })