Major update, solve bugs and add tests with bigger coverage. All deta…

.Rbuildignore

@@ -1,21 +1,25 @@
-..Rcheck
+^.*\.Rcheck$
+^.*\.tar\.gz$
 ^renv$
 ^renv\.lock$
-^Rpackage\.Rproj$
+^\.Rprofile$
+^\.Rhistory$
 ^\.Rproj\.user$
-^HDAnalyzeR\.Rproj$
-^inst\extdata$
-^inst\CITATION
+^.*\.Rproj$
+^\.DS_Store$
+.*/\.DS_Store$
+^inst/extdata$
+^inst/cheatsheet$
+^inst/hdanalyzer_app$
 ^data-raw$
 ^logo$
 ^\.github$
 ^_pkgdown\.yml$
 ^LICENSE\.md$
-^inst\cheatsheet$
-^inst\hdanalyzer_app$
 ^paper$
-^index.md
+^index\.md$
 ^case_studies$
 ^vignettes$
 ^docs$
 ^pkgdown$
+^codecov\.yml$

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

@@ -2,32 +2,48 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main]
+    branches: [main, master, 'dev/**', 'ka/**']
   pull_request:
-    branches: [main]
+  workflow_dispatch:
 
 name: R-CMD-check
 
 permissions: read-all
 
+# A newer push to the same branch makes an in-flight run obsolete.
+concurrency:
+  group: R-CMD-check-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
+    # R-devel is reported for information only: Bioconductor (limma and the
+    # optional enrichment packages) regularly lags behind R-devel for weeks
+    # after a release, which used to turn the whole matrix red.
+    continue-on-error: ${{ matrix.config.r == 'devel' }}
+
+    timeout-minutes: 90
+
     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'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      # Never turn a warning into a hard failure just because a Suggests
+      # package is momentarily unavailable on a given platform.
+      _R_CHECK_FORCE_SUGGESTS_: false
 
     steps:
       - uses: actions/checkout@v4
@@ -39,6 +55,9 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
+          # Required for the Bioconductor dependencies (limma, clusterProfiler, ...)
+          bioc-version: ${{ matrix.config.r == 'devel' && 'devel' || 'release' }}
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
@@ -47,4 +66,5 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          build_args: 'c("--no-manual","--no-build-vignettes")'
+          args: 'c("--no-manual", "--as-cran", "--ignore-vignettes")'

.github/workflows/pkgdown.yaml

@@ -8,7 +8,7 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown.yaml
+name: pkgdown
 
 permissions: read-all
 
@@ -18,6 +18,7 @@ jobs:
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    timeout-minutes: 90
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     permissions:
@@ -30,6 +31,9 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          # The site builds the reference index, which loads the Bioconductor
+          # dependencies via the package examples.
+          bioc-version: release
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -40,9 +44,36 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
+      # pkgdown renders every article in a callr subprocess. When that
+      # subprocess dies without writing to stderr (killed, out of memory, or
+      # crashed in a compiled dependency), pkgdown's own error formatter fails
+      # with `subscript out of bounds` in wrap_rmarkdown_error() and the real
+      # cause never reaches the log. The two enrichment articles peak at around
+      # 3 GB each because clusterProfiler loads the whole GO database, so a
+      # memory problem is worth ruling in or out explicitly.
+      - name: Runner resources
+        if: always()
+        run: |
+          free -h || true
+          df -h . || true
+
+      # Re-render in this process, where the error and its traceback survive.
+      # Only on failure, so a healthy build pays nothing for it.
+      - name: Re-render articles to surface the real error
+        if: failure()
+        run: |
+          for (rmd in list.files("vignettes", pattern = "[.]Rmd$", full.names = TRUE)) {
+            cat("\n==== ", rmd, " ====\n", sep = "")
+            elapsed <- system.time(
+              rmarkdown::render(rmd, output_dir = tempdir(), quiet = TRUE)
+            )[["elapsed"]]
+            cat("rendered in ", round(elapsed), "s\n", sep = "")
+          }
+        shell: Rscript {0}
+
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           clean: false
           branch: gh-pages

.gitignore

@@ -4,6 +4,11 @@ logo/
 paper/
 case_studies/data
 
+# Build and check artefacts
+*.Rcheck/
+*.tar.gz
+Rplots.pdf
+
 # Files
 .RData
 .Rproj.user

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: HDAnalyzeR
 Title: Streamlining Data Analysis for Biomarker Research
-Version: 1.0.1
+Version: 1.1.0
 Authors@R: 
     c(
       person("Konstantinos", "Antonopoulos", , "k.antono@outlook.com", 
@@ -10,24 +10,22 @@ Authors@R:
       person("Mathias", "Uhlen", , "mathias.uhlen@scilifelab.se", role = c("aut", "cph", "fnd"),
              comment = c(ORCID = "0000-0002-4858-8056"))
     )
-Description: HDAnalyzeR accelerates and simplifies data analysis for biomarker discovery in disease research. It offers a streamlined suite of tools for tasks including differential expression analysis, classification modeling, dimensionality reduction, imputation, and data visualization. With user-friendly functions and high-quality, publication-ready plots, HDAnalyzeR enables researchers—from clinicians to bioinformaticians—to efficiently explore and interpret omics data, uncovering potential biomarkers in blood plasma with ease and accuracy.
+Description: Accelerates and simplifies data analysis for biomarker discovery in
+    disease research. Offers a streamlined suite of tools for tasks including
+    differential expression analysis, classification modeling, dimensionality
+    reduction, imputation, and data visualization. With user-friendly functions and
+    high-quality, publication-ready plots, it enables researchers—from clinicians to
+    bioinformaticians—to efficiently explore and interpret omics data, uncovering
+    potential biomarkers in blood plasma with ease and accuracy.
 License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 biocViews: DifferentialExpression, Visualization, Classification
-Imports: 
-    arrow,
+Imports:
     broom,
-    cluster,
-    clusterProfiler,
     dials,
     dplyr,
-    easyPubMed (>= 3.0),
-    enrichplot,
-    embed,
     forcats,
-    fpc,
     ggbeeswarm,
     ggnewscale,
     ggplot2,
@@ -37,17 +35,10 @@ Imports:
     ggridges,
     glmnet,
     grDevices,
-    knitr,
     limma,
-    missForest,
-    multiROC,
     parsnip,
-    patchwork,
-    ppsr,
     ranger,
-    purrr,
     readr,
-    readxl,
     recipes,
     rlang,
     rsample,
@@ -58,27 +49,37 @@ Imports:
     tidygraph,
     tidyheatmaps,
     tidyr,
-    tidyselect,
     tidytext,
     tune,
-    umap,
     UpSetR,
     utils,
-    vip,
-    viridis,
-    WGCNA,
     withr,
     workflows,
-    writexl,
     yardstick
-Suggests: 
+Suggests:
+    arrow,
+    cluster,
+    clusterProfiler,
+    easyPubMed (>= 3.0),
+    embed,
+    enrichplot,
+    fpc,
+    knitr,
+    missForest,
     org.Hs.eg.db,
+    patchwork,
+    ppsr,
     ReactomePA,
+    readxl,
     rmarkdown,
     testthat (>= 3.0.0),
+    viridis,
+    WGCNA,
+    writexl
 Config/testthat/edition: 3
 Depends: 
     R (>= 4.5.0)
 LazyData: true
-URL: https://kantonopoulos.github.io/HDAnalyzeR, https://github.com/kantonopoulos/HDAnalyzeR, https://kantonopoulos.github.io/HDAnalyzeR/
+URL: https://kantonopoulos.github.io/HDAnalyzeR/, https://github.com/kantonopoulos/HDAnalyzeR
 BugReports: https://github.com/kantonopoulos/HDAnalyzeR/issues
+Config/roxygen2/version: 8.0.0