From cb6ab99b81c48d7a50bd7fd06b61b91ba341690a Mon Sep 17 00:00:00 2001 From: ake123 Date: Wed, 22 Apr 2026 15:39:38 +0300 Subject: [PATCH 01/11] update --- DESCRIPTION | 5 +++++ Dockerfile | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0d9be53..16a1a12 100644 --- a/DESCRIPTION +++ b/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, diff --git a/Dockerfile b/Dockerfile index 97c8357..2f58a1c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,4 +6,4 @@ 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 = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())" +RUN Rscript -e "options(repos = BiocManager::repositories()); devtools::install('.', dependencies=TRUE, build_vignettes=TRUE)" From 64dd8a1bee860cf30e66904c35a41c82e675c7d4 Mon Sep 17 00:00:00 2001 From: ake123 Date: Wed, 22 Apr 2026 15:44:09 +0300 Subject: [PATCH 02/11] test --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 2f58a1c..97c8357 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,4 +6,4 @@ 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()); devtools::install('.', dependencies=TRUE, build_vignettes=TRUE)" +RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())" From 279615d8e9085355889b6a7ba4fc7bdb7096e5ab Mon Sep 17 00:00:00 2001 From: ake123 Date: Wed, 22 Apr 2026 15:47:11 +0300 Subject: [PATCH 03/11] testing --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 97c8357..6053496 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,4 +6,4 @@ 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 = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())" +RUN Rscript -e "options(repos = BiocManager::repositories()); devtools::install('.', dependencies = TRUE, build_vignettes = TRUE)" From a5b7b1fab53ae8a31b34aaf06af172229562830e Mon Sep 17 00:00:00 2001 From: ake123 Date: Wed, 22 Apr 2026 15:50:49 +0300 Subject: [PATCH 04/11] correction --- Dockerfile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/Dockerfile b/Dockerfile index 6053496..2d77a28 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,4 +6,8 @@ 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 "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)" From 4ea2336473438d0bc42eb4ec6b56e8b4e6a5cb78 Mon Sep 17 00:00:00 2001 From: ake123 Date: Wed, 22 Apr 2026 16:01:01 +0300 Subject: [PATCH 05/11] update workflow --- .github/workflows/basic_checks.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index 34a527e..1f72fec 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -19,6 +19,12 @@ 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) From e8272c290210ac8204a7aa3fcd3429f4f3f81f8d Mon Sep 17 00:00:00 2001 From: ake123 Date: Wed, 22 Apr 2026 20:34:55 +0300 Subject: [PATCH 06/11] update docker --- Dockerfile | 2 +- vignettes/eurobioc2024.Rmd | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 2d77a28..8ef20f3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,7 +4,7 @@ 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 "install.packages('remotes', repos = 'https://cloud.r-project.org')" diff --git a/vignettes/eurobioc2024.Rmd b/vignettes/eurobioc2024.Rmd index f1ea3c4..43c65ab 100644 --- a/vignettes/eurobioc2024.Rmd +++ b/vignettes/eurobioc2024.Rmd @@ -1,5 +1,8 @@ --- title: EuroBioC 2024 +output: + BiocStyle::html_document: + toc: true vignette: > %\VignetteIndexEntry{EuroBioC 2024} %%\VignetteEngine{quarto::html} From fda159aa4650260be1f4d9862cf968e6f849c4a8 Mon Sep 17 00:00:00 2001 From: ake123 Date: Wed, 22 Apr 2026 22:15:45 +0300 Subject: [PATCH 07/11] update some workflows --- .github/workflows/basic_checks.yaml | 26 +++++++++++++++++++++----- vignettes/biocasia2025.Rmd | 1 + 2 files changed, 22 insertions(+), 5 deletions(-) diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index 1f72fec..270ec48 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -40,18 +40,34 @@ jobs: restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r- - name: Install dependencies + run: | + options(repos = BiocManager::repositories()) + remotes::install_deps( + dependencies = TRUE, + repos = BiocManager::repositories() + ) + shell: Rscript {0} + + - name: Install optional dependencies run: | - BiocManager::repositories() - remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) - remotes::install_cran("rcmdcheck") + 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(".")' diff --git a/vignettes/biocasia2025.Rmd b/vignettes/biocasia2025.Rmd index b608597..2747f01 100644 --- a/vignettes/biocasia2025.Rmd +++ b/vignettes/biocasia2025.Rmd @@ -439,6 +439,7 @@ differentially abundant (and prevalent) features. ```{r} #| label: calculate_daa +#| eval: false #| message: false #| warning: false library(maaslin3) From 8b4cf4cdf6cfff3b3f296d9229063fcbd18d240b Mon Sep 17 00:00:00 2001 From: ake123 Date: Wed, 22 Apr 2026 22:17:38 +0300 Subject: [PATCH 08/11] update some workflows --- .github/workflows/basic_checks.yaml | 37 +++++++++++++---------------- 1 file changed, 16 insertions(+), 21 deletions(-) diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index 270ec48..23267ff 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -27,8 +27,13 @@ jobs: - 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 @@ -40,7 +45,7 @@ jobs: restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r- - name: Install dependencies - run: | + run: | options(repos = BiocManager::repositories()) remotes::install_deps( dependencies = TRUE, @@ -68,31 +73,30 @@ jobs: 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: ${{ secrets.GITHUB_TOKEN }} - BRANCH: gh-pages # The branch the action should deploy to. - FOLDER: docs # The folder the action should deploy. + BRANCH: gh-pages + FOLDER: docs docker-build-and-push: - #needs: r-build-and-check + needs: r-build-and-check runs-on: ubuntu-latest permissions: contents: read packages: write - # This is used to complete the identity challenge - # with sigstore/fulcio when running outside of PRs. id-token: write steps: @@ -104,16 +108,13 @@ jobs: REPO_LOWER="$(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 @@ -121,8 +122,6 @@ jobs: - 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 @@ -131,16 +130,12 @@ 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 From a3c5b6544e283c900c6ebd758b5a07608f0424cd Mon Sep 17 00:00:00 2001 From: ake123 Date: Wed, 22 Apr 2026 22:22:02 +0300 Subject: [PATCH 09/11] update the workflows --- .github/workflows/basic_checks.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index 23267ff..0238b0d 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -92,7 +92,6 @@ jobs: FOLDER: docs docker-build-and-push: - needs: r-build-and-check runs-on: ubuntu-latest permissions: contents: read From fcab31d4f8f4e4c01bb28f016eb5d7bee9db2269 Mon Sep 17 00:00:00 2001 From: ake123 Date: Thu, 23 Apr 2026 08:33:14 +0300 Subject: [PATCH 10/11] update wfs --- Dockerfile | 2 +- vignettes/biocasia2025.Rmd | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 8ef20f3..2d77a28 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,7 +4,7 @@ WORKDIR /home/rstudio COPY --chown=rstudio:rstudio . /home/rstudio/ -RUN Rscript -e "options(repos = BiocManager::repositories()); BiocManager::install(ask = FALSE)" +RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask=FALSE)" RUN Rscript -e "install.packages('remotes', repos = 'https://cloud.r-project.org')" diff --git a/vignettes/biocasia2025.Rmd b/vignettes/biocasia2025.Rmd index 2747f01..9edb4dd 100644 --- a/vignettes/biocasia2025.Rmd +++ b/vignettes/biocasia2025.Rmd @@ -459,6 +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") From 687d927315caa9ad8627559d50afe6cc078fb618 Mon Sep 17 00:00:00 2001 From: ake123 Date: Thu, 23 Apr 2026 08:33:52 +0300 Subject: [PATCH 11/11] update wfs --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 2d77a28..8ef20f3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,7 +4,7 @@ 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 "install.packages('remotes', repos = 'https://cloud.r-project.org')"