Merge pull request #198 from cs50/r

Adds support for R, tidied Dockerfile

Dockerfile

@@ -1,13 +1,54 @@
-# Build statge
+# Build stage
 FROM ubuntu:22.04 as builder
 ARG DEBIAN_FRONTEND=noninteractive
 
 
+# Stage-wide dependencies
+RUN apt update && \
+    apt install --no-install-recommends --no-install-suggests --yes \
+        build-essential \
+        ca-certificates \
+        curl
+
+
+# Install Java 21.x
+# http://jdk.java.net/21/
+RUN cd /tmp && \
+    if [ $(uname -m) = "x86_64" ]; then ARCH="x64"; else ARCH="aarch64"; fi && \
+    curl --remote-name https://download.java.net/java/GA/jdk21.0.2/f2283984656d49d69e91c558476027ac/13/GPL/openjdk-21.0.2_linux-${ARCH}_bin.tar.gz && \
+    tar xzf openjdk-21.0.2_linux-${ARCH}_bin.tar.gz && \
+    rm --force openjdk-21.0.2_linux-${ARCH}_bin.tar.gz && \
+    mv jdk-21.0.2 /opt/jdk && \
+    mkdir --parent /opt/bin && \
+    ln --symbolic /opt/jdk/bin/* /opt/bin/ && \
+    chmod a+rx /opt/bin/*
+
+
+# Install Node.js 21.x
+# https://nodejs.dev/en/download/
+# https://github.com/tj/n#installation
+RUN curl --location https://raw.githubusercontent.com/tj/n/master/bin/n --output /usr/local/bin/n && \
+    chmod a+x /usr/local/bin/n && \
+    n 21.6.1
+
+
+# Install Node.js packages
+RUN npm install --global \
+    http-server
+
+
+# Patch index.js in http-server
+COPY index.js.patch /tmp
+RUN cd /usr/local/lib/node_modules/http-server/lib/core/show-dir && \
+    patch index.js < /tmp/index.js.patch && \
+    rm --force /tmp/index.js.patch
+
+
 # Suggested build environment for Python, per pyenv, even though we're building ourselves
 # https://github.com/pyenv/pyenv/wiki#suggested-build-environment
 RUN apt update && \
     apt install --no-install-recommends --no-install-suggests --yes \
-        curl ca-certificates build-essential git \
+        build-essential ca-certificates curl git \
         libssl-dev libbz2-dev libreadline-dev libsqlite3-dev \
         llvm libncursesw5-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev \
         make tk-dev unzip wget xz-utils zlib1g-dev
@@ -16,7 +57,7 @@ RUN apt update && \
 # Install Python 3.11.x
 # https://www.python.org/downloads/
 RUN cd /tmp && \
-    curl https://www.python.org/ftp/python/3.11.7/Python-3.11.7.tgz --output Python-3.11.7.tgz && \
+    curl --remote-name https://www.python.org/ftp/python/3.11.7/Python-3.11.7.tgz && \
     tar xzf Python-3.11.7.tgz && \
     rm --force Python-3.11.7.tgz && \
     cd Python-3.11.7 && \
@@ -31,14 +72,32 @@ RUN cd /tmp && \
     pip3 install --no-cache-dir --upgrade pip
 
 
+# Install R
+# https://docs.posit.co/resources/install-r-source/#build-and-install-r
+# https://cran.rstudio.com/src/base/R-4/
+RUN sed --in-place "/^#.*deb-src.*universe$/s/^# //g" /etc/apt/sources.list && \
+    apt update && \
+    apt build-dep --yes r-base && \
+    cd /tmp && \
+    curl --remote-name https://cran.rstudio.com/src/base/R-4/R-4.3.2.tar.gz && \
+    tar xzf R-4.3.2.tar.gz && \
+    rm --force R-4.3.2.tar.gz && \
+    cd R-4.3.2 && \
+    ./configure --enable-memory-profiling --enable-R-shlib && \
+    make && \
+    make install && \
+    cd .. && \
+    rm --force --recursive R-4.3.2
+
+
 # Install Ruby 3.2.x
 # https://www.ruby-lang.org/en/downloads/
 RUN apt update && \
     apt install --no-install-recommends --no-install-suggests --yes \
         autoconf \
         libyaml-dev && \
     apt clean && \
-    rm -rf /var/lib/apt/lists/* && \
+    rm --force --recursive /var/lib/apt/lists/* && \
     cd /tmp && \
     curl https://cache.ruby-lang.org/pub/ruby/3.2/ruby-3.2.2.tar.gz --output ruby-3.2.2.tar.gz && \
     tar xzf ruby-3.2.2.tar.gz && \
@@ -66,64 +125,33 @@ RUN gem install --no-document \
 # https://www.sqlite.org/howtocompile.html#compiling_the_command_line_interface
 COPY shell.c.patch /tmp
 RUN cd /tmp && \
-    curl --remote-name https://www.sqlite.org/2023/sqlite-amalgamation-3440200.zip && \
-    unzip sqlite-amalgamation-3440200.zip && \
-    rm --force sqlite-amalgamation-3440200.zip && \
-    cd sqlite-amalgamation-3440200 && \
+    curl --remote-name https://www.sqlite.org/2024/sqlite-amalgamation-3450000.zip && \
+    unzip sqlite-amalgamation-3450000.zip && \
+    rm --force sqlite-amalgamation-3450000.zip && \
+    cd sqlite-amalgamation-3450000 && \
     patch shell.c < /tmp/shell.c.patch && \
     gcc -D HAVE_READLINE -D SQLITE_DEFAULT_FOREIGN_KEYS=1 -D SQLITE_OMIT_DYNAPROMPT=1 shell.c sqlite3.c -lpthread -ldl -lm -lreadline -lncurses -o /usr/local/bin/sqlite3 && \
     cd .. && \
-    rm --force --recursive sqlite-amalgamation-3440200 && \
+    rm --force --recursive sqlite-amalgamation-3450000 && \
     rm --force /tmp/shell.c.patch
 
 
-# Install Java 21.x
-# http://jdk.java.net/21/
-RUN cd /tmp && \
-    curl --remote-name https://download.java.net/java/GA/jdk21.0.1/415e3f918a1f4062a0074a2794853d0d/12/GPL/openjdk-21.0.1_linux-x64_bin.tar.gz && \
-    tar xzf openjdk-21.0.1_linux-x64_bin.tar.gz && \
-    rm --force openjdk-21.0.1_linux-x64_bin.tar.gz && \
-    mv jdk-21.0.1 /opt/ && \
-    mkdir --parent /opt/bin && \
-    ln --symbolic /opt/jdk-21.0.1/bin/* /opt/bin/ && \
-    chmod a+rx /opt/bin/*
-
-
-# Install Node.js 21.x
-# https://nodejs.dev/en/download/
-# https://github.com/tj/n#installation
-RUN curl --location https://raw.githubusercontent.com/tj/n/master/bin/n --output /usr/local/bin/n && \
-    chmod a+x /usr/local/bin/n && \
-    n 21.5.0
-
-
-# Install GitHub CLI
-# https://github.com/cli/cli/blob/trunk/docs/install_linux.md#debian-ubuntu-linux-raspberry-pi-os-apt
-RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg && \
-    chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg && \
-    echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null && \
-    apt update && \
-    apt install gh --no-install-recommends --no-install-suggests --yes
-
-
 # Final stage
 FROM ubuntu:22.04
 LABEL maintainer="[email protected]"
 ARG DEBIAN_FRONTEND=noninteractive
 
 
 # Copy files from builder
-COPY --from=builder /usr /usr
 COPY --from=builder /opt /opt
+COPY --from=builder /usr/local /usr/local
 
 
 # Avoid "delaying package configuration, since apt-utils is not installed"
 # Install locales
 RUN apt update && \
     apt install --no-install-recommends --no-install-suggests --yes \
         apt-utils \
-        curl \
-        ca-certificates \
         locales && \
     locale-gen \
         en_US.utf8 \
@@ -145,16 +173,18 @@ RUN apt update && \
 ENV LANG=C.UTF-8
 
 
-# Install CS50, Ubuntu, and Python packages
-RUN curl https://packagecloud.io/install/repositories/cs50/repo/script.deb.sh | bash && \
-    apt update && \
+# Install Ubuntu packages
+RUN apt update && \
+    apt upgrade --yes && \
     apt install --no-install-recommends --no-install-suggests --yes \
         astyle \
         bash-completion \
         build-essential `# dpkg-dev, libc, gcc, g++, make, etc.`\
+        ca-certificates \
         clang \
         coreutils `# For fold` \
         cowsay \
+        curl \
         dos2unix \
         dnsutils `# For nslookup` \
         fonts-noto-color-emoji `# For render50` \
@@ -163,7 +193,7 @@ RUN curl https://packagecloud.io/install/repositories/cs50/repo/script.deb.sh |
         git-lfs \
         jq \
         less \
-        libcs50 \
+        liblapack3 `# For R` \
         libmagic-dev `# For style50` \
         libpango-1.0-0 libharfbuzz0b libpangoft2-1.0-0 `# For render50` \
         libyaml-0-2 `# Runtime package for gem` \
@@ -178,9 +208,19 @@ RUN curl https://packagecloud.io/install/repositories/cs50/repo/script.deb.sh |
         unzip \
         valgrind \
         vim \
+        wget \
         zip && \
-        apt clean && \
-    pip3 install --no-cache-dir \
+        apt clean
+
+
+# Install CS50 library
+RUN curl https://packagecloud.io/install/repositories/cs50/repo/script.deb.sh | bash && \
+    apt update && \
+    apt install --yes libcs50
+
+
+# Install Python packages
+RUN pip3 install --no-cache-dir \
         autopep8 \
         black \
         "check50<4" \
@@ -196,16 +236,13 @@ RUN curl https://packagecloud.io/install/repositories/cs50/repo/script.deb.sh |
         "submit50<4"
 
 
-# Install Node.js packages
-RUN npm install --global \
-    [email protected] `# Fixate for patch`
-
-
-# Patch index.js in http-server
-COPY index.js.patch /tmp
-RUN cd /usr/local/lib/node_modules/http-server/lib/core/show-dir && \
-    patch index.js < /tmp/index.js.patch && \
-    rm --force /tmp/index.js.patch
+# Install GitHub CLI (after builder stage, because writes to /usr/share)
+# https://github.com/cli/cli/blob/trunk/docs/install_linux.md#debian-ubuntu-linux-raspberry-pi-os-apt
+RUN curl --fail --location --show-error --silent https://cli.github.com/packages/githubcli-archive-keyring.gpg | dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg && \
+    chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg && \
+    echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null && \
+    apt update && \
+    apt install --no-install-recommends --no-install-suggests --yes gh
 
 
 # Copy files to image
@@ -245,4 +282,4 @@ ONBUILD USER ubuntu
 # Set user
 USER ubuntu
 WORKDIR /home/ubuntu
-ENV WORKDIR=/home/ubuntu
+ENV WORKDIR=/home/ubuntu

etc/profile.d/cli.sh

@@ -25,6 +25,7 @@ if [ "$(whoami)" != "root" ]; then
     alias mv="mv -i"
     alias pip="pip --no-cache-dir"
     alias python="python -q"
+    alias R="R --vanilla"
     alias rm="rm -i"
     alias sudo="sudo " # Trailing space enables elevated command to be an alias
 

shell.c.patch

@@ -1,9 +1,4 @@
-# diff shell.c shell_modified.c > shell.c.patch
-29321,29323c29321,29323
-<       oputf("SQLite version %s %.19s%s\n" /*extra-version-info*/
+29438,29440d29437
+<       sputf(stdout, "SQLite version %s %.19s%s\n" /*extra-version-info*/
 <             "Enter \".help\" for usage hints.\n",
 <             sqlite3_libversion(), sqlite3_sourceid(), SHELL_CIO_CHAR_SET);
----
->       //oputf("SQLite version %s %.19s%s\n" /*extra-version-info*/
->       //      "Enter \".help\" for usage hints.\n",
->       //      sqlite3_libversion(), sqlite3_sourceid(), SHELL_CIO_CHAR_SET);