Merge pull request #237 from josschavezf/dev

fix warnings from biocchek and add github workflow
drieslab · Sep 26, 2024 · cf5558a · cf5558a
2 parents c0cca85 + a348a4a
commit cf5558a
Show file tree

Hide file tree

Showing 25 changed files with 302 additions and 43 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,206 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [dev]
+  pull_request:
+    branches: [dev]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+
+
+      - name: Install reticulate
+        run: |
+          Rscript -e "install.packages('reticulate')"
+      
+      - name: Create miniconda
+        run: |
+          Rscript -e "reticulate::install_miniconda()"
+          Rscript -e "reticulate::conda_install(packages = 'scipy')"
+          
+      - name: Install pak
+        run: |
+          Rscript -e "install.packages('pak')"
+          
+      - name: Install remotes
+        run: |
+          Rscript -e "install.packages('remotes')"
+      
+      - name: Install GiottoUtils
+        run: |
+          Rscript -e "remotes::install_github('drieslab/GiottoUtils@dev')"
+      
+      - name: Install GiottoData
+        run: |
+          Rscript -e "remotes::install_github('drieslab/GiottoData')"
+          
+      - name: Install rcmdcheck
+        run: |
+          Rscript -e "install.packages('rcmdcheck')"
+      
+      - name: Install knitr
+        run: |
+          Rscript -e "install.packages('knitr')"
+      
+      - name: Install rmarkdown
+        run: |
+          Rscript -e "install.packages('rmarkdown')"
+      
+      - name: Install testthat
+        run: |
+          Rscript -e "install.packages('testthat')"
+
+      - name: Install BiocCheck
+        run: |
+          Rscript -e "install.packages('BiocManager')"
+          Rscript -e "BiocManager::install('BiocCheck')"
+      
+      - name: Install dbscan
+        run: |
+          Rscript -e "BiocManager::install('dbscan')"
+      
+      - name: Install deldir
+        run: |
+          Rscript -e "BiocManager::install('deldir')"
+      
+      - name: Install igraph
+        run: |
+          Rscript -e "BiocManager::install('igraph')"
+      
+      - name: Install magick
+        run: |
+          Rscript -e "BiocManager::install('magick')"
+      
+      - name: Install matrixStats
+        run: |
+          Rscript -e "BiocManager::install('matrixStats')"
+      
+      - name: Install sp
+        run: |
+          Rscript -e "BiocManager::install('sp')"
+      
+      - name: Install terra
+        run: |
+          Rscript -e "BiocManager::install('terra')"
+      
+      - name: Install scattermore
+        run: |
+          Rscript -e "install.packages('scattermore')"
+      
+      - name: Install exactextractr
+        run: |
+          Rscript -e "install.packages('exactextractr')"
+      
+      - name: Install future.apply
+        run: |
+          Rscript -e "BiocManager::install('future.apply')"
+          
+      - name: Install stars
+        run: |
+          Rscript -e "BiocManager::install('stars')"
+      
+      - name: Install qs
+        run: |
+          Rscript -e "BiocManager::install('qs')"
+      
+      - name: Install RTriangle
+        run: |
+          Rscript -e "BiocManager::install('RTriangle')"
+      
+      - name: Install geometry
+        run: |
+          Rscript -e "BiocManager::install('geometry')"
+      
+      - name: Install Seurat
+        run: |
+          Rscript -e "BiocManager::install('Seurat')"
+      
+      - name: Install chihaya
+        run: |
+          Rscript -e "BiocManager::install('chihaya')"
+      
+      - name: Install DelayedArray
+        run: |
+          Rscript -e "BiocManager::install('DelayedArray')"
+          
+      - name: Install DelayedMatrixStats
+        run: |
+          Rscript -e "BiocManager::install('DelayedMatrixStats')"
+          
+      - name: Install HDF5Array
+        run: |
+          Rscript -e "BiocManager::install('HDF5Array')"
+          
+      - name: Install rgl
+        run: |
+          Rscript -e "BiocManager::install('rgl')"
+          
+      - name: Install rhdf5
+        run: |
+          Rscript -e "BiocManager::install('rhdf5')"
+      
+      - name: Install S4Vectors
+        run: |
+          Rscript -e "BiocManager::install('S4Vectors')"
+      
+      - name: Install ScaledMatrix
+        run: |
+          Rscript -e "BiocManager::install('ScaledMatrix')"
+          
+      - name: Install SingleCellExperiment
+        run: |
+          Rscript -e "BiocManager::install('SingleCellExperiment')"
+          
+      - name: Install SpatialExperiment
+        run: |
+          Rscript -e "BiocManager::install('SpatialExperiment')"
+      
+      - name: Install STexampleData
+        run: |
+          Rscript -e "BiocManager::install('STexampleData')"
+      
+      - name: Install SummarizedExperiment
+        run: |
+          Rscript -e "BiocManager::install('SummarizedExperiment')"
+
+      - name: Run BiocCheck
+        run: |
+          Rscript -e "BiocCheck::BiocCheck()"
+      
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+
diff --git a/R/auxilliary.R b/R/auxilliary.R
@@ -1346,7 +1346,6 @@ calculateMetaTableCells <- function(
 #'     name = "norm_scaled_mean_metafeat"
 #' )
 #' showGiottoSpatEnrichments(g)
-#' @seealso [GiottoVisuals::spatCellPlot()]
 #' @export
 createMetafeats <- function(
         gobject,

diff --git a/R/classes.R b/R/classes.R
@@ -507,7 +507,7 @@ updateGiottoObject <- function(gobject) {
 # ! Any slot modifications should also be reflected in packedGiotto class !
 
 #' @title S4 giotto Class
-#' @description \pkg{Giotto}'s core object that encapsulates all the components
+#' @description Giotto's core object that encapsulates all the components
 #' of a spatial-omic project and facilitates analyses.
 #' @concept giotto object
 #' @slot expression expression information
@@ -1670,6 +1670,7 @@ giottoLargeImage <- setClass(
 #' transforms
 #' @slot funs list of functions associated with the object. Primarily to
 #' perform the delayed/lazy operations
+#' @returns giottoAffineImage
 setClass(
     "giottoAffineImage",
     contains = c("giottoLargeImage"),

diff --git a/R/combine_metadata.R b/R/combine_metadata.R
@@ -9,7 +9,7 @@
 #' @title combineMetadata
 #' @name combineMetadata
 #' @description This function combines the cell metadata with spatial locations
-#' and enrichment results from \code{\link[Giotto]{runSpatialEnrich}}
+#' and enrichment results from runSpatialEnrich.
 #' @param gobject Giotto object
 #' @param spat_unit spatial unit
 #' @param feat_type feature type

diff --git a/R/create.R b/R/create.R
@@ -1297,8 +1297,8 @@ create_expr_obj <- function(
         provenance = NULL,
         misc = NULL) {
     deprecate_soft("3.3.0",
-        what = "Giotto::create_expr_obj()",
-        with = "Giotto::createExprObj()"
+        what = "create_expr_obj()",
+        with = "createExprObj()"
     )
 
     if (is.null(exprMat)) exprMat <- matrix()
@@ -1370,8 +1370,8 @@ create_cell_meta_obj <- function(
         feat_type = "rna",
         provenance = NULL) {
     deprecate_soft("3.3.0",
-        what = "Giotto::create_cell_meta_obj()",
-        with = "Giotto::createCellMetaObj()"
+        what = "create_cell_meta_obj()",
+        with = "createCellMetaObj()"
     )
 
     if (is.null(col_desc)) col_desc <- NA_character_
@@ -1450,8 +1450,8 @@ create_feat_meta_obj <- function(
         feat_type = "rna",
         provenance = NULL) {
     deprecate_soft("3.3.0",
-        what = "Giotto::create_feat_meta_obj()",
-        with = "Giotto::createFeatMetaObj()"
+        what = "create_feat_meta_obj()",
+        with = "createFeatMetaObj()"
     )
 
     if (is.null(col_desc)) col_desc <- NA_character_
@@ -1541,8 +1541,8 @@ create_dim_obj <- function(
         misc = NULL,
         my_rownames = NULL) {
     deprecate_soft("3.3.0",
-        what = "Giotto::create_dim_obj()",
-        with = "Giotto::createDimObj()"
+        what = "create_dim_obj()",
+        with = "createDimObj()"
     )
 
     if (is.null(reduction_method)) reduction_method <- NA_character_
@@ -1638,8 +1638,8 @@ create_nn_net_obj <- function(
         provenance = NULL,
         misc = NULL) {
     deprecate_soft("3.3.0",
-        what = "Giotto::create_nn_net_obj()",
-        with = "Giotto::createNearestNetObj()"
+        what = "create_nn_net_obj()",
+        with = "createNearestNetObj()"
     )
 
     if (is.null(nn_type)) nn_type <- NA_character_
@@ -1717,8 +1717,8 @@ create_spat_locs_obj <- function(
         provenance = NULL,
         misc = NULL) {
     deprecate_soft("3.3.0",
-        what = "Giotto::create_spat_locs_obj()",
-        with = "Giotto::createSpatLocsObj()"
+        what = "create_spat_locs_obj()",
+        with = "createSpatLocsObj()"
     )
 
     # DT vars
@@ -1826,8 +1826,8 @@ create_spat_net_obj <- function(
         provenance = NULL,
         misc = NULL) {
     deprecate_soft("3.3.0",
-        what = "Giotto::create_spat_net_obj()",
-        with = "Giotto::createSpatNetObj()"
+        what = "create_spat_net_obj()",
+        with = "createSpatNetObj()"
     )
 
     if (is.null(method)) method <- NA_character_
@@ -1912,8 +1912,8 @@ create_spat_enr_obj <- function(
         provenance = NULL,
         misc = NULL) {
     deprecate_soft("3.3.0",
-        what = "Giotto::create_spat_enr_obj()",
-        with = "Giotto::createSpatEnrObj()"
+        what = "create_spat_enr_obj()",
+        with = "createSpatEnrObj()"
     )
 
     if (is.null(method)) method <- NA_character_

diff --git a/R/generics.R b/R/generics.R
@@ -64,7 +64,6 @@ setGeneric("reconnect", function(x, ...) standardGeneric("reconnect"))
 if (!isGeneric("nrow")) setOldClass("nrow")
 if (!isGeneric("ncol")) setOldClass("ncol")
 if (!isGeneric("dim")) setOldClass("dim")
-# if(!isGeneric('t')) setOldClass('t', where = as.environment("package:Giotto"))
 
 ## colnames and rownames generics ####
 if (!isGeneric("colnames")) setOldClass("colnames")

diff --git a/R/methods-extract.R b/R/methods-extract.R
@@ -117,7 +117,7 @@ NULL
 #'     cell_ids = c("GAATCGCCGGACACGG-1", "GAGGGCATCGCGTATC-1")
 #' )
 #' subset(g, Gfap + Gna12 > 10)
-#'
+#' @returns giotto object
 NULL
 
 #' @title Subset `giotto` subobjects
@@ -149,15 +149,15 @@ NULL
 #' # return as a subset giotto object with drop = FALSE
 #' g[[, "raw", drop = FALSE]]
 #' g[[spat_unit = "aggregate", drop = FALSE]]
-#' 
+#' @returns giotto subobject
 NULL
 
 # --------------------------------------------------------------------------- #
 
 # $ S4 access generic ####
 
 ## * coordDataDT ####
-
+#' @describeIn subset_dollar Subset giotto object
 setMethod(
     "$", signature("giotto"), function(x, name) {
         spatValues(x, feats = name)[[name]]
@@ -1173,6 +1173,7 @@ setMethod(
     }
 )
 
+#' @describeIn subset_giotto Subset giotto objects
 setMethod(
     "[", signature(x = "giotto", i = "missing", j = "missing", drop = "missing"),
     function(x, ...) {
@@ -1481,6 +1482,7 @@ sliceGiotto <- function(
 
 #' @name as.list
 #' @title Coerce to a list
+#' @aliases as.list,giotto
 #' @description Generic to coerce to a list if possible
 #' @param x the object to coerce
 #' @param slots character vector. Which data slots to include in list. See
@@ -1494,6 +1496,7 @@ sliceGiotto <- function(
 #' `"spatial_info", "spatial_locs", "spatial_network", "feat_info",
 #' "expression", "cell_metadata", "feat_metadata", "spatial_enrichment",
 #' "nn_network", "dimension_reduction", "multiomics"`
+#' @returns list
 #' @export
 setMethod("as.list", signature("giotto"), function(
         x, slots, spat_unit = NULL, feat_type = NULL, name = NULL, ...