merge in devel branch

Merge branch 'devel' into update/docs

# Conflicts:
#	docs/tutorials/multi_r_compilation.md

.Rprofile

@@ -0,0 +1,14 @@
+# Set site library for full use of VSCode-R extension.
+# This is where packages required by VSCode-R extension are installed, specifically
+# - jsonlite and rlang for R Session Watcher (needed to open HTML help pages)
+# - languageserver for code completion
+# - httpgd for http graphics device
+# These are built and installed for the default R version when container is built.
+
+.Library.site <- "/usr/local/lib/R/site-library"
+# .libPaths() already includes site library for default R version.
+.libPaths(c(.libPaths(), .Library.site))
+
+# For PNG graphics uncomment following lines
+# options(vsc.use_httpgd = FALSE,
+#         vsc.dev.args = list(width = 800, height = 600))

.devcontainer/devcontainer.json

@@ -2,21 +2,24 @@
 // README at: https://github.com/devcontainers/templates/tree/main/src/cpp 
 {
 	"name": "R-Dev-Env",
-	"image": "ghcr.io/r-devel/r-dev-env:add-version-number-to-container",
+	"image": "ghcr.io/r-devel/r-dev-env:devel",
 	"hostRequirements": {
 		"cpus": 4
 	},
 
 	"customizations": {
-		"vscode": {
+	    "vscode": {
 			"settings": {
+			    "r.lsp.diagnostics": false,
+			    "r.plot.useHttpgd": true,
 				"r.rpath.linux": "/usr/bin/R",
-        "r.rterm.linux": "/usr/bin/R",
-        "workbench.editorAssociations": {   
-           "*.md": "vscode.markdown.preview.editor"
-        },   
+				"r.rterm.linux": "/usr/bin/R",
+				"terminal.integrated.sendKeybindingsToShell": true,
 				"svn.multipleFolders.enabled": true,
-				"r.lsp.diagnostics": false
+                "workbench.editorAssociations": {   
+                    "*.md": "vscode.markdown.preview.editor"
+                },
+                "workbench.welcomePage.walkthroughs.openOnInstall": false
 			},
 			"extensions": [
 				"REditorSupport.r",
@@ -25,7 +28,6 @@
 				"ms-vscode.cpptools",
 				"MS-vsliveshare.vsliveshare"
 			]
-
 		}
 	},
 	"postCreateCommand":"cat /workspaces/r-dev-env/scripts/welcome_msg.sh >> ~/.bashrc && bash /workspaces/r-dev-env/scripts/localscript.sh"

.github/workflows/build-and-publish-image.yml

@@ -1,64 +1,66 @@
-# This workflow uses actions that are not certified by GitHub.  
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.  
-
-name: Build and publish Docker image
-
-on:
-  pull_request:
-    branches: ["devel"]
-    types: [closed]
-    paths:
-      - 'dockerfile'
-      - 'reinstall-cmake.sh'
-
-
-env:
-  REGISTRY: ghcr.io
-  IMAGE_NAME: ${{ github.repository }}
-
-jobs:
-  build-and-push-image:
-    if: ${{github.event_name == 'pull_request' && github.event.action == 'closed' && github.event.pull_request.merged == true}}
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - name: Extract version number
-        run: |
-          VER=$(cat VERSION)
-          echo "VERSION=$VER" >> $GITHUB_ENV
-
-      - name: Log in to the Container registry
-        uses: docker/login-action@v3
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@v5
-        with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-          tags: |
-            type=ref,event=branch
-            type=ref,event=pr
-            type=semver,pattern={{ env.VERSION }}
-            type=sha
-
-      - name: Build and push Docker image
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          push: true
-          build-args: |
-            "CONTAINER_VERSION=${{ env.VERSION }}"
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+# This workflow uses actions that are not certified by GitHub.  
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.  
+
+name: Build and publish Docker image
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches: ["devel"]
+    types: [closed]
+    paths:
+      - '.github/workflows/build-and-publish-image.yml'
+      - 'Dockerfile'
+      - 'reinstall-cmake.sh'
+
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    if: ${{github.event_name == 'pull_request' && github.event.action == 'closed' && github.event.pull_request.merged == true}}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Extract version number
+        run: |
+          VER=$(cat VERSION)
+          echo "VERSION=$VER" >> $GITHUB_ENV
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ github.repository }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{ env.VERSION }}
+            type=sha
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.ref_name }}
+          build-args: |
+            CONTAINER_VERSION=${{ env.VERSION }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/build-mkdocs-website.yml

@@ -1,10 +1,12 @@
 name: Build MKDocs website
 
 on:
+  workflow_dispatch:
   pull_request:
     branches: ["devel"]
     types: [closed]
     paths:
+      - 'build-mkdocs-website.yml'
       - 'docs/**/**'
       - 'mkdocs.yml'
 

.github/workflows/schedule-docker-build.yml

@@ -3,7 +3,7 @@
 # separate terms of service, privacy policy, and support
 # documentation.  
 
-name: Build and publish Docker image(Schedule Workflow)
+name: Build and publish Docker image (Schedule Workflow)
 
 on:
   pull_request:

.gitignore

@@ -3,4 +3,5 @@ R-4.1.3.tar.gz
 R-devel/
 R-devel.tar.gz
 /venv
-.cache/
+.cache/
+.Rproj.user

Dockerfile

@@ -17,14 +17,17 @@ RUN sed -i.bak "/^#.*deb-src.*universe$/s/^# //g" /etc/apt/sources.list \
     && apt -y install subversion \
     && apt -y build-dep r-base-dev \
     && apt -y install r-base-dev \
-    && Rscript -e "install.packages('languageserver', repos='https://cran.rstudio.com')"
+    && Rscript -e "install.packages('languageserver', repos='https://cran.rstudio.com')" \
+    && Rscript -e "install.packages('httpgd', repos='https://cran.rstudio.com')"
 
 RUN apt install shellcheck
 RUN apt install -y ccache
 #RUN /usr/sbin/update-ccache-symlinks
 #RUN echo 'export PATH="/usr/lib/ccache:$PATH"' | tee -a /home/vscode/.bashrc
-ENV BUILDDIR='/workspaces/r-dev-env/build'
-ENV TOP_SRCDIR='/workspaces/r-dev-env/svn'
+
+
+ENV BUILDDIR="/workspaces/r-dev-env/build/r-devel"
+ENV TOP_SRCDIR="/workspaces/r-dev-env/svn/r-devel"
 ENV PATCHDIR='/workspaces/r-dev-env/patches'
 ARG CONTAINER_VERSION
-ENV CONTAINER_VERSION ${CONTAINER_VERSION}
+ENV CONTAINER_VERSION ${CONTAINER_VERSION}

INIT

@@ -0,0 +1,3 @@
+This file is used as a marker to indicate when a codespace is first opened.
+
+See `scripts/welcome_message.sh` for use.

docs/contributor_guide/contributing_to_docs.md

@@ -17,7 +17,7 @@ source ./venv/bin/activate
 
 5. Now install libraries and dependencies for mkdocs
 ```
-pip install mkdocs mkdocs-material[imaging]
+pip install mkdocs "mkdocs-material[imaging]"
 ```
 
 6. After setting up the virtual environment and installing necessary libraries, navigate to the root directory of the project where the `mkdocs.yml` file is located.
@@ -32,3 +32,5 @@ This will compile the documentation and serve it locally. You can access the doc
 
 9. Preview Changes: As you make changes, the local development server will automatically detect them and update the preview in real-time. Refresh your browser to see the changes.
 
+**N.B.** There is a known issue with mkdocs not alwayds finding Cairo. The issue and suggested fixes are on the [MkDocs Image Processing](https://squidfunk.github.io/mkdocs-material/plugins/requirements/image-processing/) page.
+

docs/tutorials/multi_r_compilation.md

@@ -66,8 +66,7 @@ You can build multiple R versions in the same Codespaces environment.
     Enter the number corresponding to the selected version: 
     ```
 
-
-!!! Note 
+!!! Note
 
     `BUILDDIR` and `TOP_SRCDIR` will be set to the defaults using the label `r-devel` 
     whenever a new bash terminal is opened, e.g. when the codespace is restarted.

docs/tutorials/svn_help.md

@@ -1,3 +1,50 @@
-# SVN Help Command
+## Checking out a different revision
 
-svn commands and desc somewhere here
+You can check out a specific revision of the R sources with
+
+```bash
+svn checkout -r 1234 https://svn.r-project.org/R/trunk/ $TOP_SRCDIR
+```
+
+### Finding the last revision that passed check
+
+Occasionally, the latest revision of the R sources does not pass `make check`. 
+In this case, it can be a good idea to revert to an earlier revision until the R Core Team have made further updates to fix the issue.
+
+Visit the [Build from SVN](https://github.com/r-devel/r-svn/actions/workflows/build-svn.yaml) page that summarises attempted builds of R using GitHub actions on the unofficial GitHub mirror. 
+Find the latest run that completed successfully (green checkmark) and use the commit message to search for the corresponding Subversion revision.
+For example, to search the last 10 revisions for the log message "More @apifun and such annotations"
+
+```bash
+cd $TOP_SRCDIR
+svn log --limit 10 --search "More @apifun and such annotations"
+```
+```
+/workspaces/r-dev-env/svn/r-devel $ svn log --limit 10 --search "More @apifun and such annotations"
+------------------------------------------------------------------------
+r86726 | luke | 2024-06-12 18:00:19 +0000 (Wed, 12 Jun 2024) | 2 lines
+
+More @apifun and such annotations.
+
+------------------------------------------------------------------------
+r86723 | luke | 2024-06-11 20:31:36 +0000 (Tue, 11 Jun 2024) | 2 lines
+
+More @apifun and such annotations.
+
+------------------------------------------------------------------------
+```
+
+If you have already attempted to build R, you can re-run the make with the version identified in your search as follows:
+
+```
+svn checkout -r 86726 https://svn.r-project.org/R/trunk/ $TOP_SRCDIR
+cd $BUILDDIR
+make
+make check
+```
+
+Otherwise, follow the full instructions in [Building R](./building_r.md), updating the svn checkout command to use the required revision.
+
+## Further Subversion Help
+
+For further help on Subversion, refer to the online book [Version Control with Subversion](https://svnbook.red-bean.com/).

scripts/localscript.sh

@@ -3,12 +3,11 @@
 mkdir -p /home/vscode/.local/bin
 mkdir -p $PATCHDIR
 
-chmod +x /workspaces/r-dev-env/scripts/rterm.sh
-chmod +x /workspaces/r-dev-env/scripts/multi_r.sh
+chmod +x /workspaces/r-dev-env/scripts/which_r.sh
+chmod +x /workspaces/r-dev-env/scripts/set_build_r.sh
 
-mv /workspaces/r-dev-env/scripts/rterm.sh /home/vscode/.local/bin/rterm
-cp /workspaces/r-dev-env/scripts/multi_r.sh /home/vscode/.local/bin/multi_r
+cp /workspaces/r-dev-env/scripts/which_r.sh /home/vscode/.local/bin/which_r
+cp /workspaces/r-dev-env/scripts/set_build_r.sh /home/vscode/.local/bin/set_build_r
 
-#remove git directory
-cd /workspaces/r-dev-env
+# remove git directory
 rm -rf .git