More R CMD check fixes

multimeric · multimeric · commit 98a94267170c · 2022-12-23T22:24:23.000+11:00
diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,4 @@ HCAquery.Rproj
 split_files.makeflow
 ._*
 .DS_Store
+inst/doc
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -24,7 +24,8 @@ Imports:
     assertthat,
     SeuratObject,
     Seurat,
-    methods
+    methods,
+    rlang
 Suggests:
     here,
     stringr,
@@ -38,7 +39,9 @@ Suggests:
     tools,
     rmarkdown,
     zellkonverter,
-    dbplyr
+    dbplyr,
+    knitr,
+    testthat
 Biarch: true
 biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing, Transcription, Transcriptomics
 Encoding: UTF-8
@@ -47,3 +50,4 @@ RoxygenNote: 7.2.1
 LazyDataCompression: xz
 URL: https://github.com/stemangiola/HCAquery
 BugReports: https://github.com/stemangiola/HCAquery/issues
+VignetteBuilder: knitr
diff --git a/LICENCE b/LICENCE
diff --git a/NAMESPACE b/NAMESPACE
@@ -27,4 +27,5 @@ importFrom(purrr,map)
 importFrom(purrr,map_int)
 importFrom(purrr,reduce)
 importFrom(purrr,when)
+importFrom(rlang,.data)
 importFrom(tidySingleCellExperiment,inner_join)
diff --git a/R/query.R b/R/query.R
@@ -4,6 +4,7 @@
 #' This can be obtained from the [get_metadata()] function.
 #' @param repository A character vector of length one, which is a file path to where the single cell data is stored
 #' @param genes An optional character vector of genes to return the counts for. By default counts for all genes will be returned.
+#' @param assay TODO
 #'
 #' @importFrom dplyr pull filter
 #' @importFrom tidySingleCellExperiment inner_join
@@ -16,6 +17,7 @@
 #' @importFrom SummarizedExperiment colData assayNames<-
 #' @importFrom purrr when
 #' @importFrom magrittr equals
+#' @importFrom rlang .data
 #'
 #' @export
 #'
@@ -35,7 +37,7 @@ get_SingleCellExperiment = function(
 
 	files_to_read =
 	  raw_data |>
-		pull(file_id_db) |>
+		pull(.data$file_id_db) |>
 		unique() |>
 		as.character()
 
@@ -61,7 +63,7 @@ get_SingleCellExperiment = function(
 		  sce |>
 			  inner_join(
   				# Needed because cell IDs are not unique outside the file_id or file_id_db
-  				filter(raw_data, file_id_db == .x),
+  				filter(raw_data, .data$file_id_db == .x),
   				by=".cell"
   			)
 		})
diff --git a/man/get_SingleCellExperiment.Rd b/man/get_SingleCellExperiment.Rd
diff --git a/man/get_seurat.Rd b/man/get_seurat.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1 +1,4 @@
 library(testthat)
+library(HCAquery)
+
+test_check("HCAquery")
diff --git a/tests/testthat/test-query.R b/tests/testthat/test-query.R
@@ -1,5 +1,3 @@
-library(HCAquery)
-
 test_that("The genes argument to get_SingleCellExperiment subsets genes", {
   meta = get_metadata() |> head(2)
   
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/harmonisation_workflow.Rmd b/vignettes/harmonisation_workflow.Rmd
@@ -2,7 +2,11 @@
 title: "harmonisation_workflow"
 author: "Stefano Mangiola"
 date: '2022-09-14'
-output: html_document
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{harmonisation_workflow}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r setup, include=FALSE}

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,3 @@`
`1`		`-library(HCAquery)`
`2`		`-`
`3`	`1`	`test_that("The genes argument to get_SingleCellExperiment subsets genes", {`
`4`	`2`	`meta = get_metadata() \|> head(2)`
`5`	`3`