From 8447f6f289a700ee77b08322c73afcc6ee61895d Mon Sep 17 00:00:00 2001
From: xec-cm <fcatala@irsicaixa.es>
Date: Thu, 21 Dec 2023 10:08:15 +0100
Subject: [PATCH] remove Docker setup

---
 .BBSoptions                      |  2 --
 .github/workflows/check-bioc.yml | 49 --------------------------------
 Dockerfile                       | 11 -------
 3 files changed, 62 deletions(-)
 delete mode 100644 .BBSoptions
 delete mode 100644 Dockerfile

diff --git a/.BBSoptions b/.BBSoptions
deleted file mode 100644
index dc5e4e0..0000000
--- a/.BBSoptions
+++ /dev/null
@@ -1,2 +0,0 @@
-# Generated by biocroxytest: do not edit by hand!
-RunLongTests: TRUE
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index 2d5a725..351fe8d 100644
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -289,52 +289,3 @@ jobs:
         with:
           name: ${{ runner.os }}-biocversion-devel-r-devel-results
           path: check
-
-
-  ## Code adapted from
-  ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
-  docker-build-and-push:
-    runs-on: ubuntu-latest
-    needs: build-check
-    steps:
-      - name: Checkout Repository
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: actions/checkout@v3
-
-      - name: Register repo name
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        id: reg_repo_name
-        run: |
-          echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
-
-      - name: Set up QEMU
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: docker/setup-qemu-action@v2
-
-      - name: Set up Docker Buildx
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: docker/setup-buildx-action@v2
-
-      - name: Login to Docker Hub
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
-      ## account, not your actual dockerhub account password. You can get it
-      ## from https://hub.docker.com/settings/security.
-      ## Check https://github.com/docker/build-push-action/tree/v4.0.0
-      ## for more details.
-      ## Alternatively, try checking
-      ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
-
-      - name: Build and Push Docker
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
-        uses: docker/build-push-action@v4
-        with:
-          context: .
-          push: true
-          tags: >
-            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
-            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 77d1c42..0000000
--- a/Dockerfile
+++ /dev/null
@@ -1,11 +0,0 @@
-FROM bioconductor/bioconductor_docker:devel
-
-WORKDIR /home/rstudio
-
-COPY --chown=rstudio:rstudio . /home/rstudio/
-
-ENV R_REMOTES_NO_ERRORS_FROM_WARNINGS=true
-ENV CRAN="https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"
-
-RUN Rscript -e "BiocManager::install(update = TRUE, ask=FALSE)"
-RUN Rscript -e "devtools::install(dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())"