Merge branch 'devel' of https://github.com/microbiome/mia into import…

…_functions

.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: ${{ true }}
+        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 }}

R/estimateDivergence.R

@@ -145,13 +145,13 @@ setMethod("estimateDivergence", signature = c(x="SummarizedExperiment"),
         if( "median" %in% reference || "mean" %in% reference ){
             reference <- apply(mat, 1, reference)
         } else if( !reference %in% colnames(mat) ) {
-            stop(paste("Reference", reference, "not recognized."))
+            stop("Reference ", reference, " not recognized.", call. = FALSE)
         }
     }
 
     # Distance between all samples against one reference sample
     # FIXME: could be be optimzed with sweep / parallelization
     v <- seq_len(ncol(mat))
-    sapply(v, function (i) {FUN(rbind(mat[,i], reference), method=method, ...)})
+    vapply(v, function (i) {FUN(rbind(mat[,i], reference), method=method, ...)},FUN.VALUE = numeric(1))
 }
 

R/estimateDiversity.R

@@ -216,7 +216,7 @@
 #' plotColData(tse, "Shannon")
 #' # ... by sample type
 #' plotColData(tse, "Shannon", "SampleType")
-#' \dontrun{
+#' \donttest{
 #' # combining different plots
 #' library(patchwork)
 #' plot_index <- c("Shannon","GiniSimpson")

R/estimateDominance.R

@@ -184,7 +184,7 @@
 #'
 #' # Indices must be written correctly (e.g. dbp, not dbp), otherwise an error
 #' # gets thrown
-#' \dontrun{esophagus <- estimateDominance(esophagus, index="dbp")}
+#' \donttest{esophagus <- estimateDominance(esophagus, index="dbp")}
 #' # Calculates dbp and Core Abundance indices
 #' esophagus <- estimateDominance(esophagus, index=c("dbp", "core_abundance"))
 #' # Shows all indices

R/estimateRichness.R

@@ -178,7 +178,7 @@
 #'
 #' # Indices must be written correctly (all lowercase), otherwise an error
 #' # gets thrown
-#' \dontrun{esophagus <- estimateRichness(esophagus, index="ace")}
+#' \donttest{esophagus <- estimateRichness(esophagus, index="ace")}
 #'
 #' # Calculates Chao1 and ACE indices only
 #' esophagus <- estimateRichness(esophagus, index=c("chao1", "ace"),