From 525baaa4f833b71745114a9a7c8962cd4f433326 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= Date: Sat, 24 Jun 2023 15:01:11 -0700 Subject: [PATCH 1/3] Fix declarations of centroided/smoothed setters for OnDiskMSnExp objects With current R-devel (R 4.4), trying to install MSnBase <= 2.25.2 fails with error messages complaining about the declarations of the centroided<- and smoothed<- methods for OnDiskMSnExp objects. The complain is: arguments ('value') after '...' in the generic must appear in the method, in the same place at the end of the argument list This commit fixes the method delcarations so that they are compatible with R >= 4.4. --- DESCRIPTION | 2 +- R/methods-OnDiskMSnExp.R | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5d430184..987697cb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: MSnbase Title: Base Functions and Classes for Mass Spectrometry and Proteomics -Version: 2.25.2 +Version: 2.25.3 Description: MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and diff --git a/R/methods-OnDiskMSnExp.R b/R/methods-OnDiskMSnExp.R index bf9a296b..251366a1 100644 --- a/R/methods-OnDiskMSnExp.R +++ b/R/methods-OnDiskMSnExp.R @@ -184,7 +184,7 @@ setMethod("centroided", "OnDiskMSnExp", setReplaceMethod("centroided", signature(object = "OnDiskMSnExp", value = "logical"), - function(object, value, msLevel.) { + function(object, msLevel., ..., value) { if (missing(msLevel.)) { if (length(value) == 1) value <- rep(value, length(object)) @@ -223,7 +223,7 @@ setMethod("smoothed", "OnDiskMSnExp", setReplaceMethod("smoothed", signature(object = "OnDiskMSnExp", value = "logical"), - function(object, value, msLevel.) { + function(object, msLevel., ..., value) { if (missing(msLevel.)) { if (length(value) == 1) value <- rep(value, length(object)) From 0d632929d80e6f5197d25e38e1de6fedfde6d518 Mon Sep 17 00:00:00 2001 From: Laurent Gatto Date: Sun, 25 Jun 2023 13:09:19 +0200 Subject: [PATCH 2/3] update news --- NEWS.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 2870f7fd..5ca74a58 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,14 @@ # MSnbase 2.25 +## MSnbase 2.25.3 + +- Fix declarations of centroided/smoothed setters for OnDiskMSnExp + objects (from Hervé Pagès via Github). + ## MSnbase 2.25.2 - Fix bug in descendPeaks (see [#583](https://github.com/lgatto/MSnbase/issues/583)) - + ## MSnbase 2.25.1 - Fix remote mztab filename. From 274a3ed94c765fc933c9e81f958bc77733f62aba Mon Sep 17 00:00:00 2001 From: Laurent Gatto Date: Sun, 25 Jun 2023 13:11:41 +0200 Subject: [PATCH 3/3] fix version --- DESCRIPTION | 2 +- NEWS.md | 10 ++++++++-- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 987697cb..f83856f4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: MSnbase Title: Base Functions and Classes for Mass Spectrometry and Proteomics -Version: 2.25.3 +Version: 2.27.1 Description: MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and diff --git a/NEWS.md b/NEWS.md index 5ca74a58..efa0a6dd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,16 @@ -# MSnbase 2.25 +# MSnbase 2.27 -## MSnbase 2.25.3 +## MSnbase 2.27.1 - Fix declarations of centroided/smoothed setters for OnDiskMSnExp objects (from Hervé Pagès via Github). +## MSnbase 2.27.0 + +- New devel + +# MSnbase 2.25 + ## MSnbase 2.25.2 - Fix bug in descendPeaks (see [#583](https://github.com/lgatto/MSnbase/issues/583))