[r-apt]: installBspm option (#169)

Close #69 Add a new option to set up bspm.
rocker-org · Aug 5, 2023 · 6149004 · 6149004
1 parent 1e2af2d
commit 6149004
Show file tree

Hide file tree

Showing 6 changed files with 75 additions and 1 deletion.
diff --git a/src/r-apt/NOTES.md b/src/r-apt/NOTES.md
@@ -52,6 +52,17 @@ Packages that cannot be installed via apt must be installed using the R function
 
 For more information, please check [the Rocker Project website](https://rocker-project.org/use/extending.html).
 
+
+### Binary installation via R with bspm
+
+If set the `installBspm` option to `true`, this Feature will install and set up
+the [`bspm` R package](https://github.com/Enchufa2/bspm).
+
+`bspm` provides functions to manage packages via the distribution's package manager.
+
+Known limitation: `bspm` does not seem to work correctly on Debian.
+(<https://github.com/rocker-org/devcontainer-features/pull/169#issuecomment-1665839740>)
+
 ## Python package installation
 
 This feature has some options to install Python packages such as `jupyterlab`.

diff --git a/src/r-apt/devcontainer-feature.json b/src/r-apt/devcontainer-feature.json
@@ -1,7 +1,7 @@
 {
 	"name": "R (via apt)",
 	"id": "r-apt",
-	"version": "0.3.4",
+	"version": "0.4.0",
 	"description": "Installs the latest R, some R packages, and needed dependencies. Note: May require source code compilation for some R packages.",
 	"documentationURL": "https://github.com/rocker-org/devcontainer-features/tree/main/src/r-apt",
 	"options": {
@@ -50,6 +50,11 @@
 			"type": "boolean",
 			"default": true,
 			"description": "For Debian, install packages from Debian testing. If false, the R package installed by apt may be out of date."
+		},
+		"installBspm": {
+			"type": "boolean",
+			"default": false,
+			"description": "Install and enable BSPM (Bridge to System Package Manager) to install R packages. This option is only working on Ubuntu now."
 		}
 	},
 	"installsAfter": [

diff --git a/src/r-apt/install.sh b/src/r-apt/install.sh
@@ -8,6 +8,7 @@ INSTALL_RMARKDOWN=${INSTALLRMARKDOWN:-"false"}
 INSTALL_JUPYTERLAB=${INSTALLJUPYTERLAB:-"false"}
 INSTALL_RADIAN=${INSTALLRADIAN:-"false"}
 INSTALL_VSCDEBUGGER=${INSTALLVSCDEBUGGER:-"false"}
+INSTALL_BSPM=${INSTALLBSPM:-"false"}
 
 USERNAME=${USERNAME:-${_REMOTE_USER:-"automatic"}}
 R_LIBRARY_PATH="/usr/local/lib/R/site-library"
@@ -93,6 +94,10 @@ if [ "${INSTALL_JUPYTERLAB}" = "true" ]; then
     PIP_PACKAGES+=(jupyterlab)
 fi
 
+if [ "${INSTALL_BSPM}" = "true" ]; then
+    APT_PACKAGES+=(make sudo python3-apt python3-gi)
+fi
+
 apt_get_update() {
     if [ "$(find /var/lib/apt/lists/* | wc -l)" = "0" ]; then
         echo "Running apt-get update..."
@@ -226,6 +231,12 @@ if [ "${INSTALL_VSCDEBUGGER}" = "true" ]; then
     R -q -e "pak::pkg_install('ManuelHentschel/vscDebugger@$(git ls-remote --tags https://github.com/ManuelHentschel/vscDebugger | grep -oP "v[0-9]+\\.[0-9]+\\.[0-9]+" | sort -V | tail -n 1)')"
 fi
 
+if [ "${INSTALL_BSPM}" = "true" ]; then
+    R -q -e 'install.packages("bspm")'
+    echo "options(bspm.sudo = TRUE)" >>/etc/R/Rprofile.site
+    echo "bspm::enable()" >>/etc/R/Rprofile.site
+fi
+
 # Set up IRkernel
 if [ "${INSTALL_JUPYTERLAB}" = "true" ]; then
     echo "Register IRkernel..."

diff --git a/test/r-apt/bspm-debian.sh b/test/r-apt/bspm-debian.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+set -e
+
+# Optional: Import test library bundled with the devcontainer CLI
+source dev-container-features-test-lib
+
+R -q -e 'install.packages("curl")'
+
+# Feature-specific tests
+check "R" R -q -e "sessionInfo()"
+check "R curl" R -q -e 'names(installed.packages()[, 3])' | grep curl
+
+# Report result
+reportResults
diff --git a/test/r-apt/bspm-ubuntu.sh b/test/r-apt/bspm-ubuntu.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+set -e
+
+# Optional: Import test library bundled with the devcontainer CLI
+source dev-container-features-test-lib
+
+R -q -e 'install.packages("curl")'
+
+# Feature-specific tests
+check "R" R -q -e "sessionInfo()"
+check "R curl" R -q -e 'names(installed.packages()[, 3])' | grep curl
+
+# Report result
+reportResults
diff --git a/test/r-apt/scenarios.json b/test/r-apt/scenarios.json
@@ -55,5 +55,22 @@
 				"installRadian": true
 			}
 		}
+	},
+	// TODO: enable tesing on debian
+	// "bspm-debian": {
+	// 	"image": "mcr.microsoft.com/devcontainers/base:debian",
+	// 	"features": {
+	// 		"r-apt": {
+	// 			"installBspm": true
+	// 		}
+	// 	}
+	// },
+	"bspm-ubuntu": {
+		"image": "mcr.microsoft.com/devcontainers/base:ubuntu",
+		"features": {
+			"r-apt": {
+				"installBspm": true
+			}
+		}
 	}
 }