Merge pull request #34 from stemangiola/fix-actions

Attempt to fix github actions

Author: stemangiola

.Rbuildignore

@@ -1,3 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^dev
+^\.github$
+^LICENSE\.md$

.github/workflows/check-bioc.yml

@@ -81,14 +81,14 @@ jobs:
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -149,7 +149,7 @@ jobs:
       - name: Install BiocManager
         run: |
           message(paste('****', Sys.time(), 'installing BiocManager ****'))
-          remotes::install_cran("BiocManager")
+          remotes::install_github("Bioconductor/BiocManager")
         shell: Rscript {0}
 
       - name: Set BiocVersion
@@ -270,7 +270,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v2
         with:
           name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results
           path: check

.gitignore

@@ -9,3 +9,4 @@ HCAquery.Rproj
 split_files.makeflow
 ._*
 .DS_Store
+inst/doc

DESCRIPTION

@@ -6,41 +6,42 @@ Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre"))
                   )
 Description: Queries the Human Cell Atlas.
-License: GPL-3
+License: GPL (>= 3)
 Depends:
     R (>= 4.1.0)
 Imports:
-	dplyr,
-	SummarizedExperiment,
-	SingleCellExperiment,
-	tidySingleCellExperiment,
-	purrr,
-	zellkonverter,
-	BiocGenerics,
-	glue,
-	HDF5Array,
-	DBI,
-	RSQLite,
-	dbplyr
+    dplyr,
+    SummarizedExperiment,
+    SingleCellExperiment,
+    tidySingleCellExperiment,
+    purrr,
+    BiocGenerics,
+    glue,
+    HDF5Array,
+    DBI,
+    RSQLite,
+    magrittr,
+    assertthat,
+    SeuratObject,
+    Seurat,
+    methods,
+    rlang
 Suggests:
     here,
     stringr,
-    Seurat,
     tidyseurat,
     scMerge,
     DelayedArray,
     openssl,
     cellxgenedp,
-    SingleCellExperiment,
     celldex,
     SingleR,
     tools,
     rmarkdown,
-    SeuratObject
-VignetteBuilder:
-    knitr
-RdMacros:
-    lifecycle
+    zellkonverter,
+    dbplyr,
+    knitr,
+    testthat
 Biarch: true
 biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing, Transcription, Transcriptomics
 Encoding: UTF-8
@@ -49,3 +50,4 @@ RoxygenNote: 7.2.1
 LazyDataCompression: xz
 URL: https://github.com/stemangiola/HCAquery
 BugReports: https://github.com/stemangiola/HCAquery/issues
+VignetteBuilder: knitr