update

.github/workflows/basic_checks.yaml

@@ -19,10 +19,21 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@v4
 
+      - name: Install base R helpers
+        run: |
+          options(repos = c(CRAN = Sys.getenv("CRAN")))
+          install.packages(c("BiocManager", "remotes", "pkgdown", "rcmdcheck"))
+        shell: Rscript {0}
+
       - name: Query dependencies and update old packages
         run: |
-          BiocManager::install(ask=FALSE)
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          options(repos = BiocManager::repositories())
+          BiocManager::install(ask = FALSE, update = TRUE)
+          saveRDS(
+            remotes::dev_package_deps(dependencies = TRUE),
+            ".github/depends.Rds",
+            version = 2
+          )
         shell: Rscript {0}
 
       - name: Cache R packages
@@ -35,42 +46,56 @@ jobs:
 
       - name: Install dependencies
         run: |
-          BiocManager::repositories()
-          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
-          remotes::install_cran("rcmdcheck")
+          options(repos = BiocManager::repositories())
+          remotes::install_deps(
+            dependencies = TRUE,
+            repos = BiocManager::repositories()
+          )
         shell: Rscript {0}
 
+      - name: Install optional dependencies
+        run: |
+          options(repos = BiocManager::repositories())
+          BiocManager::install("ANCOMBC", ask = FALSE, update = FALSE)
+          install.packages("biclust")
+        shell: Rscript {0}
+        continue-on-error: true
+
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
+          _R_CHECK_FORCE_SUGGESTS_: false
+        run: |
+          options(repos = BiocManager::repositories())
+          rcmdcheck::rcmdcheck(
+            args = c("--no-manual"),
+            error_on = "warning",
+            check_dir = "check"
+          )
         shell: Rscript {0}
 
       - name: Build pkgdown
         run: |
-           PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'
+          Rscript -e 'pkgdown::build_site(".")'
 
-      # deploy needs rsync? Seems so.
       - name: Install deploy dependencies
         run: |
           apt-get update
           apt-get -y install rsync
 
       - name: Deploy 🚀
+        if: github.event_name != 'pull_request'
         uses: JamesIves/github-pages-deploy-action@v4
         with:
           TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          BRANCH: gh-pages # The branch the action should deploy to.
-          FOLDER: docs # The folder the action should deploy.
+          BRANCH: gh-pages
+          FOLDER: docs
 
   docker-build-and-push:
-    #needs: r-build-and-check
     runs-on: ubuntu-latest
     permissions:
       contents: read
       packages: write
-      # This is used to complete the identity challenge
-      # with sigstore/fulcio when running outside of PRs.
       id-token: write
 
     steps:
@@ -82,25 +107,20 @@ jobs:
           REPO_LOWER="$(echo "${{ github.repository }}" | tr '[:upper:]' '[:lower:]')"
           REGISTRY=ghcr.io
           echo "BUILD_DATE=$(date +'%Y-%m-%d %H:%M:%S')" >> $GITHUB_ENV
-          echo "GIT_SHA=$(echo ${{ github.sha }} | cut -c1-7)" >> $GITHUB_ENV
+          echo "GIT_SHA=$(echo "${{ github.sha }}" | cut -c1-7)" >> $GITHUB_ENV
           echo "REGISTRY=${REGISTRY}" >> $GITHUB_ENV
           echo "IMAGE=${REGISTRY}/${REPO_LOWER}" >> $GITHUB_ENV
 
       - name: Show environment
-        run: |
-          env
+        run: env
 
-      # Install the cosign tool except on PR
-      # https://github.com/sigstore/cosign-installer
       - name: Install cosign
         if: github.event_name != 'pull_request'
         uses: sigstore/cosign-installer@v3
 
       - name: Setup Docker buildx
         uses: docker/setup-buildx-action@v3
 
-      # Login against a Docker registry except on PR
-      # https://github.com/docker/login-action
       - name: Log into registry ${{ env.REGISTRY }}
         if: github.event_name != 'pull_request'
         uses: docker/login-action@v3
@@ -109,16 +129,12 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      # Extract metadata (tags, labels) for Docker
-      # https://github.com/docker/metadata-action
       - name: Extract Docker metadata
         id: meta
         uses: docker/metadata-action@v5
         with:
           images: ${{ env.IMAGE }}
 
-      # Build and push Docker image with Buildx (don't push on PR)
-      # https://github.com/docker/build-push-action
       - name: Build and push Docker image
         id: build-and-push
         uses: docker/build-push-action@v5

DESCRIPTION

@@ -26,6 +26,7 @@ Suggests:
     BiocManager,
     BiocParallel,
     BiocPkgTools,
+    BiocStyle,
     Biostrings,
     bluster,
     caret,
@@ -61,6 +62,8 @@ Suggests:
     mia,
     miaTime,
     miaViz,
+    miaSim,
+    miaDash,
     microbiomeDataSets,
     MicrobiomeStat,
     mikropml,
@@ -78,6 +81,7 @@ Suggests:
     quarto,
     RColorBrewer,
     rebook,
+    rmarkdown,
     reshape2,
     reticulate,
     rgl,
@@ -101,6 +105,7 @@ Remotes:
     github::microbiome/miaViz,
     github::microbiome/miaTime,
     github::joey711/phyloseq,
+    github::biobakery/maaslin3,
     github::stefpeschel/NetCoMi,
     github::zdk123/SpiecEasi,
     github::GraceYoon/SPRING,

Dockerfile

@@ -4,6 +4,10 @@ WORKDIR /home/rstudio
 
 COPY --chown=rstudio:rstudio . /home/rstudio/
 
-RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask=FALSE)"
+RUN Rscript -e "options(repos = BiocManager::repositories()); BiocManager::install(ask = FALSE)"
 
-RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())"
+RUN Rscript -e "install.packages('remotes', repos = 'https://cloud.r-project.org')"
+
+RUN Rscript -e "remotes::install_version('biclust', version = '2.0.3.1', repos = 'https://cran.r-project.org', upgrade = 'never')"
+
+RUN Rscript -e "options(repos = BiocManager::repositories()); devtools::install('.', dependencies = TRUE, build_vignettes = TRUE)"

vignettes/biocasia2025.Rmd

@@ -439,6 +439,7 @@ differentially abundant (and prevalent) features.
 
 ```{r}
 #| label: calculate_daa
+#| eval: false
 #| message: false
 #| warning: false
 library(maaslin3)
@@ -458,6 +459,7 @@ The function generates different outputs. The output includes summary plot in
 a directory that was specified by `output` argument.
 
 ```{r}
+#| eval: false
 #| label: visualize_daa
 library(knitr)
 file_path <- file.path("maaslin3_output", "figures", "summary_plot.png")

vignettes/eurobioc2024.Rmd

@@ -1,5 +1,8 @@
 ---
 title: EuroBioC 2024
+output:
+  BiocStyle::html_document:
+    toc: true
 vignette: >
   %\VignetteIndexEntry{EuroBioC 2024}
   %%\VignetteEngine{quarto::html}