Bugfix/working pkg installation

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,34 @@
+# 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: 
+      - '**' # This matches all branches
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

@@ -9,3 +9,5 @@ src/*.so
 src/*.dll
 *.Rcheck/
 analysis/
+*.o
+*.so

R/RcppExports.R

@@ -8,10 +8,10 @@ NULL
 NULL
 
 .pairwise_col_diff_cpp <- function(x, col_names) {
-    .Call('_biomarkerPanels_pairwise_col_diff_cpp', PACKAGE = 'biomarkerPanels', x, col_names)
+    .Call(`_biomarkerPanels_pairwise_col_diff_cpp`, x, col_names)
 }
 
 .pairwise_ratios_cpp <- function(x, feature_col, feature_name, other_names) {
-    .Call('_biomarkerPanels_pairwise_ratios_cpp', PACKAGE = 'biomarkerPanels', x, feature_col, feature_name, other_names)
+    .Call(`_biomarkerPanels_pairwise_ratios_cpp`, x, feature_col, feature_name, other_names)
 }
 

data-raw/simulate_gene_expression.R → data-raw/simulated_gene_expression.R

@@ -1,11 +1,13 @@
+## code to prepare `simulated_gene_expression` dataset goes here
+
 #!/usr/bin/env Rscript
 
 # Simulate four log-scale gene expression datasets with dataset-specific shifts
 # and save them alongside binary response labels.
 
 set.seed(20240220)
 
-n_features <- 5000L
+n_features <- 500L
 n_samples <- 100L
 n_datasets <- 4L
 dataset_ids <- seq_len(n_datasets)
@@ -81,7 +83,7 @@ for (i in dataset_ids) {
 names(x_list) <- sprintf("x%d", dataset_ids)
 names(y_list) <- sprintf("y%d", dataset_ids)
 
-output <- list(
+simulated_gene_expression <- list(
   metadata = list(
     seed = 20240220,
     n_samples = n_samples,
@@ -95,6 +97,5 @@ output <- list(
   y_list = y_list
 )
 
-saveRDS(output, file = "simulated_gene_expression.Rds")
-
 cat("Simulation complete. Saved to simulated_gene_expression.Rds\n")
+usethis::use_data(simulated_gene_expression, compress = "xz")

moo.Rproj

@@ -0,0 +1,18 @@
+Version: 1.0
+ProjectId: a48d3ba8-5f77-4365-83ec-cb7d9519c322
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

vignettes/getting-started.Rmd

@@ -6,8 +6,10 @@ output:
     toc: true
 vignette: >
   %\VignetteIndexEntry{Getting Started with biomarkerPanels}
-  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+editor_options: 
+  chunk_output_type: console
 ---
 
 ```{r setup, include=FALSE}
@@ -53,28 +55,37 @@ package build, these files would live in `inst/extdata/`; here we reuse the
 fixture directly.
 
 ```{r load-fixture}
-fixture_candidates <- c(
-  system.file("extdata", "fake_gene_expression.Rds", package = "biomarkerPanels"),
-  system.file("test-data", "fake_gene_expression.Rds", package = "biomarkerPanels"),
-  file.path("..", "tests", "data", "fake_gene_expression.Rds"),
-  file.path("..", "..", "tests", "data", "fake_gene_expression.Rds")
-)
-fixture_candidates <- fixture_candidates[nzchar(fixture_candidates)]
-fixture_path <- NULL
-for (candidate in fixture_candidates) {
-  if (file.exists(candidate)) {
-    fixture_path <- candidate
-    break
-  }
-}
-if (is.null(fixture_path)) {
-  stop(
-    "Unable to locate `fake_gene_expression.Rds`. ",
-    "Regenerate it via `data-raw/simulate_gene_expression.R` if needed.",
-    call. = FALSE
-  )
-}
-cohorts <- readRDS(fixture_path)
+# fixture_path <- system.file("test-data", "fake_gene_expression.Rds", package = "biomarkerPanels")
+# if (fixture_path == "") {
+#   fixture_path <- file.path("./tests", "data", "fake_gene_expression.Rds")
+# }
+# stopifnot(file.exists(fixture_path)) # didn't exist for some reason. 
+# cohorts <- readRDS("/dskh/nobackup/harryr/moo/tests/data/fake_gene_expression.Rds")
+data(simulated_gene_expression, package = "biomarkerPanels")
+cohorts = simulated_gene_expression
+
+# fixture_candidates <- c(
+#   system.file("extdata", "fake_gene_expression.Rds", package = "biomarkerPanels"),
+#   system.file("test-data", "fake_gene_expression.Rds", package = "biomarkerPanels"),
+#   file.path("..", "tests", "data", "fake_gene_expression.Rds"),
+#   file.path("..", "..", "tests", "data", "fake_gene_expression.Rds")
+# )
+# fixture_candidates <- fixture_candidates[nzchar(fixture_candidates)]
+# fixture_path <- NULL
+# for (candidate in fixture_candidates) {
+#   if (file.exists(candidate)) {
+#     fixture_path <- candidate
+#     break
+#   }
+# }
+# if (is.null(fixture_path)) {
+#   stop(
+#     "Unable to locate `fake_gene_expression.Rds`. ",
+#     "Regenerate it via `data-raw/simulate_gene_expression.R` if needed.",
+#     call. = FALSE
+#   )
+# }
+# cohorts <- readRDS(fixture_path)
 
 lapply(cohorts$x_list, dim)
 colnames(cohorts$x_list[[1]])[1:6]