Add MsBackendMetaboLights

.github/workflows/check-bioc.yml

@@ -22,7 +22,8 @@
 
 on:
  push:
- pull_request:
+ paths-ignore:
+ - 'README.md'
 
 name: R-CMD-check-bioc
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MsBackendMetaboLights
 Title: Retrieve Mass Spectrometry Data from MetaboLights
-Version: 0.0.1
+Version: 0.0.3
 Authors@R:
  c(person(given = "Johannes", family = "Rainer",
  email = "Johannes.Rainer@eurac.edu",
@@ -21,13 +21,20 @@ Description: MetaboLights is one of the main public repositories for storage
 Depends:
  R (>= 4.2.0)
 Imports:
- curl
+ curl,
+ ProtGenerics,
+ Spectra,
+ BiocFileCache,
+ methods
 Suggests:
  testthat,
  rmarkdown,
- mzR
+ mzR,
+ knitr,
+ BiocStyle
 License: Artistic-2.0
 Encoding: UTF-8
+VignetteBuilder: knitr
 BugReports: https://github.com/RforMassSpectrometry/MsBackendMetaboLights/issues
 URL: https://github.com/RforMassSpectrometry/MsBackendMetaboLights
 biocViews: Infrastructure, MassSpectrometry, Metabolomics, DataImport, Proteomics

NAMESPACE

@@ -1,8 +1,23 @@
 # Generated by roxygen2: do not edit by hand
 
+export(MsBackendMetaboLights)
 export(mtbls_ftp_path)
 export(mtbls_list_files)
+exportClasses(MsBackendMetaboLights)
+exportMethods(backendInitialize)
+exportMethods(backendMerge)
+importClassesFrom(Spectra,MsBackendMzR)
+importFrom(BiocFileCache,BiocFileCache)
+importFrom(ProtGenerics,backendMerge)
 importFrom(curl,curl)
 importFrom(curl,handle_setopt)
 importFrom(curl,new_handle)
+importFrom(methods,callNextMethod)
+importFrom(methods,new)
 importFrom(utils,read.table)
+importMethodsFrom(BiocFileCache,"bfcmeta<-")
+importMethodsFrom(BiocFileCache,bfcmetalist)
+importMethodsFrom(BiocFileCache,bfcquery)
+importMethodsFrom(BiocFileCache,bfcrpath)
+importMethodsFrom(ProtGenerics,backendInitialize)
+importMethodsFrom(ProtGenerics,dataOrigin)

NEWS.md

@@ -1,5 +1,14 @@
 # MsBackendMetabolights 0.0
 
+## Changes in 0.0.3
+
+- Add vignette and `backendMerge,MsBackendMetaboLights` function.
+
+## Changes in 0.0.2
+
+- Add `MsBackendMetaboLights` class, constructor and `backendInitalize()`
+ method.
+
 ## Changes in 0.0.1
 
 - Add utility functions to retrieve information from MetaboLights.