Merge branch 'main' of github.com:PRL-PRG/r-compile-server

.devcontainer/Dockerfile

@@ -1,79 +1,70 @@
-# This Dockerfile uses separate build arguments instead of VARIANT
-ARG TARGET_JAVA_VERSION=22.0.2+9
-ARG TARGET_GNUR_VERSION=4.3.2
-ARG TARGET_DEBIAN_VERSION=bookworm
-FROM mcr.microsoft.com/devcontainers/base:$TARGET_DEBIAN_VERSION
+ARG JAVA_VERSION=22
+ARG MAVEN_VERSION=3.9.9
+ARG LLVM_VERSION=17
+ARG BASE_IMAGE=ubuntu-24.04
 
-USER root
-ARG TARGET_JAVA_VERSION
-ARG TARGET_GNUR_VERSION
-ENV JAVA_HOME=/usr/lib/jvm/jdk
-ENV PATH="$JAVA_HOME/bin:$PATH"
-# Default to UTF-8 file.encoding
-ENV LANG=en_US.UTF-8
-
-# Install OpenJDK (Adoptium / temurin)
-RUN arch="$(dpkg --print-architecture)" \
-  && case "$arch" in \
-		"amd64") \
-			arch1="x64"; \
-			;; \
-		"arm64") \
-			arch1="aarch64"; \
-			;; \
-		*) echo >&2 "error: unsupported architecture: '$arch'"; exit 1 ;; \
-	esac \
-  && jdkUrl="https://github.com/adoptium/temurin22-binaries/releases/download/jdk-$TARGET_JAVA_VERSION/OpenJDK22U-jdk_${arch1}_linux_hotspot_$(echo $TARGET_JAVA_VERSION | tr '+' '_').tar.gz" \
-  && wget --progress=dot:giga -O temurin.tar.gz "$jdkUrl" \
-  && wget --progress=dot:giga -O sha256.txt "$jdkUrl.sha256.txt"
-
-RUN sha256Text=$(cat sha256.txt) \
-  && sha256=$(expr substr "$sha256Text" 1 64) \
-  && echo "$sha256 temurin.tar.gz" | sha256sum --strict --check - \
-  && rm sha256.txt*
+FROM mcr.microsoft.com/devcontainers/base:$BASE_IMAGE
 
-RUN mkdir -p "$JAVA_HOME"
-RUN tar --extract \
-		--file temurin.tar.gz \
-		--directory "$JAVA_HOME" \
-		--strip-components 1 \
-		--no-same-owner
-RUN rm temurin.tar.gz*
-
-RUN ln -s $JAVA_HOME /docker-java-home
-RUN ln -s $JAVA_HOME /usr/local/openjdk-$(echo $TARGET_JAVA_VERSION | cut -d'-' -f1)
-
-# Install GNU-R
-# From https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Essential-and-useful-other-programs-under-a-Unix_002dalike
-ARG GNUR_RUNTIME_DEPENDENCIES="build-essential gfortran"
-ARG GNUR_BUILD_DEPENDENCIES="libreadline-dev zlib1g-dev libbz2-dev liblzma-dev libpcre2-dev"
+# default to UTF-8 file.encoding
+ENV LANG=en_US.UTF-8
 
-RUN gnurUrl="https://cloud.r-project.org/src/base/R-$(printf %.1s $TARGET_GNUR_VERSION)/R-$TARGET_GNUR_VERSION.tar.gz" \
-  && wget --progress=dot:giga -O gnur.tar.gz "$gnurUrl"
+# this is weird, but without this, the default value would not be used.
+ARG JAVA_VERSION
+ARG MAVEN_VERSION
+ARG LLVM_VERSION
 
-RUN mkdir -p /tmp/gnur
-RUN tar --extract \
-    --file gnur.tar.gz \
-    --directory /tmp/gnur \
-    --strip-components 1 \
-    --no-same-owner
-RUN rm gnur.tar.gz*
+# install OpenJDK
+RUN curl -fsSL https://packages.adoptium.net/artifactory/api/gpg/key/public | gpg --dearmor | tee /etc/apt/trusted.gpg.d/adoptium.gpg > /dev/null \
+  && echo "deb https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list \
+  && apt update -y \
+  && apt install -y temurin-$JAVA_VERSION-jdk \
+  && ln -s "$(which java | xargs readlink -f | xargs dirname | xargs dirname)" /opt/java
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get update
-RUN DEBIAN_FRONTEND=noninteractive apt-get -y install --no-install-recommends $GNUR_BUILD_DEPENDENCIES $GNUR_RUNTIME_DEPENDENCIES
+# install maven
+RUN mkdir -p /opt/maven \
+ && curl -fsSL -o /tmp/apache-maven.tar.gz "https://dlcdn.apache.org/maven/maven-3/$MAVEN_VERSION/binaries/apache-maven-$MAVEN_VERSION-bin.tar.gz" \
+ && tar -xzf /tmp/apache-maven.tar.gz -C /opt/maven --strip-components=1 \
+ && rm -f /tmp/apache-maven.tar.gz
 
-RUN cd /tmp/gnur \
- && ./tools/rsync-recommended \
- && ./configure --prefix=/usr/local --with-x=no \
- && make \
- && make install
-RUN rm -rf /tmp/gnur
+ENV MAVEN_HOME=/opt/maven
+ENV JAVA_HOME=/opt/java
+ENV PATH="$PATH:$MAVEN_HOME/bin"
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get -y remove --purge $GNUR_BUILD_DEPENDENCIES
-# Fortran is needed at
-RUN DEBIAN_FRONTEND=noninteractive apt-get -y install --no-install-recommends gfortran
-RUN DEBIAN_FRONTEND=noninteractive apt-get -y autoremove
+# install support for building client:
+# - the bundled R
+# - the rsh R package
+RUN apt update -y \
+  && apt install -y \
+    bear \
+    build-essential \
+    ca-certificates \
+    gdb \
+    gfortran \
+    libbz2-dev \
+    libcairo2-dev \
+    libcurl4-openssl-dev \
+    libgrpc++-dev \
+    libgtk2.0-dev \
+    libicu-dev \
+    libjpeg-dev \
+    liblzma-dev \
+    libpango1.0-dev \
+    libpng-dev \
+    libreadline-dev \
+    libssl-dev \
+    libtiff5-dev \
+    libx11-dev \
+    libxt-dev \
+    libxxhash-dev \
+    libzmq3-dev \
+    protobuf-compiler \
+    protobuf-compiler-grpc \
+    rr \
+    software-properties-common \
+    xvfb \
+    zlib1g-dev
 
-# [Optional] Uncomment this section to install additional OS packages.
-# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
-#     && apt-get -y install --no-install-recommends <your-package-list-here>
+# install LLVM
+RUN curl -fsSL -o /opt/llvm.sh https://apt.llvm.org/llvm.sh \
+  && chmod +x /opt/llvm.sh \
+  && /opt/llvm.sh "$LLVM_VERSION"

.devcontainer/devcontainer.json

@@ -1,14 +1,33 @@
 {
+  "name": "r-compile-server",
   "build": {
     "dockerfile": "./Dockerfile",
     "context": "."
   },
-  features: {
-    "ghcr.io/devcontainers/features/java:1": {
-      "installMaven": "true"
+  // ensure consistency between vscode and intellij
+  // the embedded R uses absolute paths
+  "workspaceMount": "source=${localWorkspaceFolder},target=/workspace,type=bind,consistency=cached",
+  "workspaceFolder": "/workspace",
+  "postCreateCommand": "make setup",
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "vscjava.vscode-java-pack",
+        "llvm-vs-code-extensions.vscode-clangd",
+        "vadimcn.vscode-lldb"
+      ]
     }
   },
-  "containerEnv": {
-    "JAVA_HOME": "/usr/lib/jvm/jdk"
+  // needed for ptrace based debuggers such as gdb / rr
+  "runArgs": [
+    "--cap-add=SYS_PTRACE",
+    "--security-opt",
+    "seccomp=unconfined"
+  ],
+  "updateRemoteUserUID": true,
+  "features": {
+    "ghcr.io/devcontainers/features/common-utils:2": {
+      "configureZshAsDefaultShell": true
+    }
   }
-}
+}

.githooks/pre-commit.sh

@@ -1,24 +1,28 @@
 #!/bin/bash
 
-everything_staged=$(git diff --name-only)
+SERVER_DIR="server"
+
+cd "$SERVER_DIR"
+
+everything_staged=$(git diff --name-only -- "$SERVER_DIR")
 # `no_partial_stages` from https://github.com/evilmartians/lefthook/issues/140#issuecomment-1012967850
-no_partial_stages=$(comm -12 <(git diff --name-only | sort) <(git diff --name-only --staged | sort))
-format_only_staged=-DspotlessFiles="$(git diff --staged --name-only | sed 's/^/.*/' | paste -sd ',' -)"
+no_partial_stages=$(comm -12 <(git diff --name-only -- "$SERVER_DIR" | sort) <(git diff --name-only --staged -- "$SERVER_DIR" | sort))
+format_only_staged=-DspotlessFiles="$(git diff --staged --name-only -- "$SERVER_DIR" | sed 's/^/.*/' | paste -sd ',' -)"
 
 if [ -n "$no_partial_stages" ]; then
-  # Format only staged changes. Don't commit if we change anything, because we can't partially format a file, and it's
-  # ambiguous what formatting changes should be staged and what shouldn't.
-  mvn spotless:check "$format_only_staged" || {
-    mvn spotless:apply "$format_only_staged"
-    echo "Reformatted a partially-staged file. Re-interactively-stage and commit again."
-    exit 1
-  }
+	# Format only staged changes. Don't commit if we change anything, because we can't partially format a file, and it's
+	# ambiguous what formatting changes should be staged and what shouldn't.
+	mvn spotless:check "$format_only_staged" || {
+		mvn spotless:apply "$format_only_staged"
+		echo "Reformatted a partially-staged file. Re-interactively-stage and commit again."
+		exit 1
+	}
 elif [ -n "$everything_staged" ]; then
-  # Format only staged changes. We must re-add them because the formats aren't committed.
-  mvn spotless:apply "$format_only_staged"
-  git diff --name-only --staged | tr \\n \\0 | xargs -0 git add -f
+	# Format only staged changes. We must re-add them because the formats aren't committed.
+	mvn spotless:apply "$format_only_staged"
+	git diff --name-only --staged -- "$SERVER_DIR" | tr \\n \\0 | xargs -0 git add -f
 else
-  # Format everything because spotless caches. We must re-add everything because the formats aren't committed.
-  mvn spotless:apply
-  git add -u
+	# Format everything because spotless caches. We must re-add everything because the formats aren't committed.
+	mvn spotless:apply
+	git add -u
 fi

.github/workflows/maven.yml

@@ -31,15 +31,19 @@ jobs:
         with:
           r-version: "4.3.2"
       - name: Build artifact
+        working-directory: server
         run: mvn --batch-mode --update-snapshots package
       - run: mkdir staging && cp target/*.jar staging
+        working-directory: server
       - name: Upload snapshot as artifact
         uses: actions/upload-artifact@v3
+        working-directory: server
         with:
           name: snapshot
           path: target/*-SNAPSHOT.jar
       # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive
       - name: Update dependency graph
+        working-directory: server
         uses: advanced-security/maven-dependency-submission-action@571e99aab1055c2e71a1e2309b9691de18d6b7d6
 
   test:
@@ -58,6 +62,7 @@ jobs:
         with:
           r-version: "4.3.2"
       - name: Run tests (no static analyses)
+        working-directory: server
         run: mvn --batch-mode --update-snapshots test
 
   verify:
@@ -76,6 +81,7 @@ jobs:
         with:
           r-version: "4.3.2"
       - name: Run tests and static analyses
+        working-directory: server
         run: mvn --batch-mode --update-snapshots verify
 
   verify-macos:
@@ -94,4 +100,5 @@ jobs:
         with:
           r-version: "4.3.2"
       - name: Run tests and static analyses
+        working-directory: server
         run: mvn --batch-mode --update-snapshots verify

.gitignore

@@ -1,47 +1,28 @@
-**/src/test/snapshots/**/*.fail*
-!src/test/resources/**/*.log
-
 ### Tempfiles ###
 .devcontainer/.features.temp.dockerfile
 
-### Build ###
-target/
-!.mvn/wrapper/maven-wrapper.jar
-!**/src/main/**/target/
-!**/src/test/**/target/
-
-### IntelliJ IDEA ###
-.idea/modules.xml
-.idea/jarRepositories.xml
-.idea/compiler.xml
-.idea/libraries/
-*.iws
-*.iml
-*.ipr
-
-### Eclipse ###
-.apt_generated
-.classpath
-.factorypath
-.project
-# We actually want to sync this
-# .settings
-.springBeans
-.sts4-cache
-
-### NetBeans ###
-/nbproject/private/
-/nbbuild/
-/dist/
-/nbdist/
-/.nb-gradle/
-build/
-!**/src/main/**/build/
-!**/src/test/**/build/
-
 ### VS Code ###
 # We actually want to sync this
 # .vscode/
 
 ### Mac OS ###
-.DS_Store
+.DS_Store
+
+### R ###
+.RData
+.Rhistory
+external/R/doc/manual/*.html
+external/R/doc/NEWS.pdf
+..Rcheck
+
+### C ###
+.cache
+.gdb_history
+compile_commands.json
+*.so
+*.o
+
+### IntelliJ IDEA ###
+/.idea/uiDesigner.xml
+.idea/modules.xml
+.idea/workspace.iml

.gitmodules

@@ -0,0 +1,7 @@
+[submodule "external/R"]
+	path = external/R
+	url = https://github.com/PRL-PRG/r-compiler-server-gnur
+	ignore = untracked
+[submodule "external/R-debug"]
+	path = external/R-debug
+	url = https://github.com/PRL-PRG/r-compiler-server-gnur