Bioconductor finalization (#26)

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* Bugfixes

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* Vignettes use preloaded data

* Update vignettes

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* Add genomes

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.github/workflows/rworkflows.yml

@@ -0,0 +1,58 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions:
+      contents: write
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: bioconductor/bioconductor_docker:devel
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release
+        - os: macOS-latest
+          bioc: devel
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: devel
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ false }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        enable_act: ${{ false }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MGnifyR
 Type: Package
-Version: 0.99.17
+Version: 0.99.18
 Authors@R:
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",
@@ -20,10 +20,10 @@ biocViews: PackageTypeData, ExperimentData, MicrobiomeData, SequencingData
 License: Artistic-2.0 | file LICENSE
 Encoding: UTF-8
 Depends:
-    R(>= 4.3),
+    R(>= 4.4.0),
     mia,
     MultiAssayExperiment,
-    TreeSummarizedExperiment (>= 1.99.3),
+    TreeSummarizedExperiment,
     SummarizedExperiment,
     biomformat,
     BiocGenerics
@@ -57,12 +57,12 @@ BugReports: https://github.com/EBI-Metagenomics/MGnifyR/issues
 VignetteBuilder: knitr
 RoxygenNote: 7.3.0
 Collate:
-    'MGnifyR.R'
-    'MgnifyClient.R'
     'utils.R'
-    'allGenerics.R'
-    'allClasses.R'
-    'allAccessors.R'
+    'MgnifyClient.R'
+    'AllGenerics.R'
+    'AllClasses.R'
+    'AllAccessors.R'
+    'MGnifyR.R'
     'deprecate.R'
     'doQuery.R'
     'getData.R'

NEWS

@@ -1,6 +1,10 @@
+Version: 0.99.18
+Date: 2024-02-12
++ Last modifications for Biocondutor submission
+
 Changes in version 0.99.17
 + Added getData function for fetching raw data from the database
 
-Changes in version 0.99.0
+Version 0.99.0
 + Support for TreeSummarizedExperiment and MultiAssayExperiment
 + Submitted to Bioconductor