Merge branch 'main' into phili

rformassspectrometry · Jan 10, 2024 · 81a8f8f · 81a8f8f
2 parents 87b9662 + 9de8e4c
commit 81a8f8f
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diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -22,7 +22,8 @@
 
 on:
   push:
-  pull_request:
+    paths-ignore:
+      - 'README.md'
 
 name: R-CMD-check-bioc
 
@@ -52,9 +53,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.17', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'next', bioc: '3.17'}
-          - { os: windows-latest, r: 'next', bioc: '3.17'}
+          - { 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: 'devel', bioc: '3.19'}
+          - { os: windows-latest, r: 'devel', bioc: '3.19'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -164,6 +165,7 @@ jobs:
           ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
           ## https://github.com/r-lib/remotes/issues/296
           ## Ideally, all dependencies should get installed in the first pass.
+          BiocManager::install("rmarkdown")
 
           ## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79
           remotes::install_github("ropensci/bibtex")

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MetaboCoreUtils
 Title: Core Utils for Metabolomics Data
-Version: 1.11.0
+Version: 1.11.1
 Description: MetaboCoreUtils defines metabolomics-related core functionality
     provided as low-level functions to allow a data structure-independent usage
     across various R packages. This includes functions to calculate between ion
@@ -44,12 +44,16 @@ Depends:
     R (>= 4.0)
 Imports:
     utils,
-    MsCoreUtils
+    MsCoreUtils,
+    BiocParallel,
+    methods,
+    stats
 Suggests:
     BiocStyle,
     testthat,
     knitr,
-    rmarkdown
+    rmarkdown,
+    robustbase
 License: Artistic-2.0
 LazyData: no
 VignetteBuilder: knitr

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,6 +4,7 @@ export(addElements)
 export(adductFormula)
 export(adductNames)
 export(adducts)
+export(adjust_lm)
 export(calculateKm)
 export(calculateKmd)
 export(calculateMass)
@@ -12,6 +13,7 @@ export(containsElements)
 export(convertMtime)
 export(correctRindex)
 export(countElements)
+export(fit_lm)
 export(formula2mz)
 export(indexRtime)
 export(internalStandardMixNames)
@@ -26,10 +28,15 @@ export(mz2mass)
 export(pasteElements)
 export(standardizeFormula)
 export(subtractElements)
+importFrom(BiocParallel,SerialParam)
+importFrom(BiocParallel,bplapply)
 importFrom(MsCoreUtils,closest)
 importFrom(MsCoreUtils,group)
 importFrom(MsCoreUtils,ppm)
+importFrom(methods,is)
 importFrom(stats,approx)
+importFrom(stats,lm)
 importFrom(stats,na.omit)
+importFrom(stats,predict)
 importFrom(stats,setNames)
 importFrom(utils,read.table)
diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,16 @@
+# MetaboCoreUtils 1.11
+
+## MetaboCoreUtils 1.11.1
+
+- Add functions to enable linear model-based adjustment of (LC-MS derived)
+  abundance matrices (issue
+  [#75](https://github.com/rformassspectrometry/MetaboCoreUtils/issues/75)).
+
 # MetaboCoreUtils 1.9
 
 ## MetaboCoreUtils 1.9.4
 
-- Add function `mclosest` (issue 
+- Add function `mclosest` (issue
   [#20](https://github.com/rformassspectrometry/MetaboCoreUtils/issues/20)).
 
 ## MetaboCoreUtils 1.9.3