Add GitHub workflow for R CMD check

.Rbuildignore

@@ -1,6 +1,10 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 
+# Git
+.gitignore
+.github
+
 # README
 README.md
 README.Rmd

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

@@ -0,0 +1,51 @@
+# Workflow derived from
+# https://github.com/r-lib/actions/blob/v2-branch/examples/check-standard.yaml
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+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: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    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
+
+      - 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
+

DESCRIPTION

@@ -56,7 +56,7 @@ biocViews: Annotation, DifferentialExpression, GeneExpression,
     Reactome, Software, Transcription, Visualization
 License: MIT + file LICENSE
 Depends:
-    R (>= 4.3.0)
+    R (>= 4.0.0)
 Imports:
     data.table (>= 1.13.0),
     dplyr,

R/set-based-enrichment-test.r

@@ -61,8 +61,7 @@ do_the_simulation <- function(list_of_all_genes, pool, select,DB, steps,
         } else { cl <- makeCluster(spec = nthread, type = "PSOCK")}
         clusterExport(cl, c("DB","list_of_all_genes", "pool", "select",
             "seeds_per_thread", "steps_per_thread"), envir = environment())
-        clusterEvalQ(cl, c("mulea", "stats", "graphics", "grDevices", "utils",
-            "datasets","methods","base"))
+        clusterEvalQ(cl, devtools::load_all())
         result_of_paralel <- clusterApplyLB(cl = cl, seq_len(nthread), 
             function(idx) {simulation_result_tbl <- tryCatch(
                 enrichment_test_simulation(DB, list_of_all_genes, pool, 

tests/testthat/testSubramanianTest.R

@@ -34,78 +34,3 @@ test_that("GSEA : no element_scores vector.", {
   testthat::expect_error(muleaTestRes <-
                            run_test(mulea_ranked_based_test_model))
 })
-
-test_that("GSEA : out of ontology elements.", {
-  set.seed(1)
-  gmtMock <- data.frame(
-    ontology_id = "GO:0000001",
-    ontology_name = "Imagin gen ontology to tests.",
-    list_of_values = I(list(c("a", "b", "c", "d"))),
-    stringsAsFactors = FALSE
-  )
-  testDataMock <- c("a", "b", "e", "f")
-  scoreDataMock <- c(0.1, 0.5, 0.7, 1)
-
-  mulea_ranked_based_test_model <- gsea(
-    gmt = gmtMock,
-    element_names = testDataMock,
-    element_scores = scoreDataMock)
-
-  testthat::expect_warning(muleaTestRes <-
-                             run_test(mulea_ranked_based_test_model))
-  testthat::expect_equal(muleaTestRes$p_value, 151/495)
-})
-
-test_that("GSEA : DB1 + DB2.", {
-  set.seed(1)
-  gmtMock1 <- data.frame(
-    ontology_id = "GO:0000001",
-    ontology_name = "Imagin gen ontology to tests.",
-    list_of_values = I(list(c("a", "b", "c", "d"))),
-    stringsAsFactors = FALSE
-  )
-  gmtMock2 <- data.frame(
-    ontology_id = "GO:0000002",
-    ontology_name = "Imagin gen ontology to tests.",
-    list_of_values = I(list(c("e", "f", "g", "h"))),
-    stringsAsFactors = FALSE
-  )
-  gmtMock <- rbind(gmtMock1, gmtMock2)
-  testDataMock <- c("d", "e", "f")
-  scoreDataMock <- c(-0.3, 0.4, 0.5)
-
-  mulea_ranked_based_test_model <- gsea(
-    gmt = gmtMock,
-    element_names = testDataMock,
-    element_scores = scoreDataMock)
-
-  muleaTestRes <- run_test(mulea_ranked_based_test_model)
-  testthat::expect_equal(muleaTestRes$p_value, c(169 / 330, 107 / 219))
-})
-
-test_that("GSEA : DB1 + DB2 out of background_element_names.", {
-  set.seed(1)
-  gmtMock1 <- data.frame(
-    ontology_id = "GO:0000001",
-    ontology_name = "Imagin gen ontology to tests.",
-    list_of_values = I(list(c("a", "b", "c", "d"))),
-    stringsAsFactors = FALSE
-  )
-  gmtMock2 <- data.frame(
-    ontology_id = "GO:0000002",
-    ontology_name = "Imagin gen ontology to tests.",
-    list_of_values = I(list(c("e", "f", "c", "d"))),
-    stringsAsFactors = FALSE
-  )
-  gmtMock <- rbind(gmtMock1, gmtMock2)
-  testDataMock <- c("b", "d", "e", "f")
-  scoreDataMock <- c(-1, 0, 0, 1)
-
-  mulea_ranked_based_test_model <- gsea(
-    gmt = gmtMock,
-    element_names = testDataMock,
-    element_scores = scoreDataMock)
-
-  muleaTestRes <- run_test(mulea_ranked_based_test_model)
-  testthat::expect_equal(muleaTestRes$p_value, c(156 / 653, 251 / 492))
-})