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chudyandrejchudyandrej
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Rebuild IR image with puthon 3.9
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4 files changed

+252
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‎.circleci/config.yml‎

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@@ -4,7 +4,6 @@ orbs:
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aws-cli: circleci/aws-cli@5.1.1
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docker: circleci/docker@2.8
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7-
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commands:
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split_python_version:
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steps:
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--output type=registry,push=true \
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.
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build-and-push-ir:
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executor: docker/docker
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parameters:
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r-version:
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type: string
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environment:
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R_VERSION: << parameters.r-version >>
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steps:
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- checkout
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- docker_login
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- split_python_version # This provides PYTHON_VERSION
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- setup_buildkit_builder
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- run:
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name: Build and push python-conda image
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command: |
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REPOSITORY="deepnote/ir"
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TAG="${R_VERSION}${CIRCLE_PULL_REQUEST:+-ra-${CIRCLE_PULL_REQUEST##*/}}"
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docker buildx build \
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--file=./ir/Dockerfile.ir \
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--tag=978928340082.dkr.ecr.us-east-1.amazonaws.com/${REPOSITORY}:${TAG} \
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--tag=docker.io/${REPOSITORY}:${TAG} \
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--build-arg R_VERSION=${R_VERSION} \
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--cache-from type=registry,ref=docker.io/${REPOSITORY}:${TAG}-buildcache,mode=max \
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--cache-to type=registry,ref=docker.io/${REPOSITORY}:${TAG}-buildcache,mode=max,image-manifest=true,oci-mediatypes=true \
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--progress plain \
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--platform linux/amd64 \
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--provenance=false \
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--sbom=false \
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--output type=registry,push=true \
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./ir
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build-and-push-gpu:
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machine:
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image: ubuntu-2404:current
@@ -216,6 +246,11 @@ python-versions: &python-versions
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- "3.10.15"
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- "3.11.10"
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r-versions: &r-versions
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- "3.5.2"
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- "4.0.4"
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- "4.2.0"
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workflows:
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build:
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jobs:
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python-version: *python-versions
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requires:
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- Building the base image
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- build-and-push-ir:
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name: R << matrix.r-version >>
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matrix:
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parameters:
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r-version: *r-versions
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- build-and-push-gpu:
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name: Tensorflow 2.9

‎ir/Dockerfile‎

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This file was deleted.

‎ir/Dockerfile.ir‎

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# Define build arguments for Python and R versions
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ARG PYTHON_VERSION=3.9
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ARG R_VERSION=4.4.0
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# Use the specified Python version as the base image
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FROM deepnote/python:${PYTHON_VERSION}
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# Set environment variables
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# Use the R version specified by the build argument
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ENV R_VERSION="${R_VERSION}" \
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R_HOME="/usr/local/lib/R" \
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TZ="Etc/UTC" \
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DEFAULT_KERNEL_NAME="ir" \
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DEEPNOTE_PYTHON_KERNEL_ONLY=""
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# Copy the R installation script and run it
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COPY install_R_source.sh /rocker_scripts/install_R_source.sh
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RUN chmod +x /rocker_scripts/install_R_source.sh && \
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/rocker_scripts/install_R_source.sh
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# Set the working directory
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WORKDIR /opt
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# Create and activate a virtual environment in one RUN command
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RUN python -m venv jupyter-env && \
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. ./jupyter-env/bin/activate && \
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pip install --upgrade pip notebook
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# Install IRkernel and configure it
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RUN . ./jupyter-env/bin/activate && \
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R -e "install.packages('IRkernel', repos='http://cran.rstudio.com/')" && \
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R -e "IRkernel::installspec()"
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# Clean up unnecessary files to reduce the image size
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RUN apt-get clean && \
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

‎ir/install_R_source.sh‎

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#!/bin/bash
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## Source of the installation file https://github.com/rocker-org/rocker-versioned2/blob/master/scripts/install_R_source.sh
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## Install R from source.
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##
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## In order of preference, first argument of the script, the R_VERSION variable.
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## ex. latest, devel, patched, 4.0.0
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##
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## 'devel' means the prerelease development version (Latest daily snapshot of development version).
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## 'patched' means the prerelease patched version (Latest daily snapshot of patched version).
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set -e
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R_VERSION=${1:-${R_VERSION:-"latest"}}
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PURGE_BUILDDEPS=${PURGE_BUILDDEPS:-"true"}
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# shellcheck source=/dev/null
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source /etc/os-release
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apt-get update
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apt-get -y install locales
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## Configure default locale
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LANG=${LANG:-"en_US.UTF-8"}
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/usr/sbin/locale-gen --lang "${LANG}"
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/usr/sbin/update-locale --reset LANG="${LANG}"
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export DEBIAN_FRONTEND=noninteractive
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R_HOME=${R_HOME:-"/usr/local/lib/R"}
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READLINE_VERSION=8
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if [ "${UBUNTU_CODENAME}" == "bionic" ]; then
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READLINE_VERSION=7
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fi
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apt-get install -y --no-install-recommends \
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bash-completion \
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ca-certificates \
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file \
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fonts-texgyre \
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g++ \
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gfortran \
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gsfonts \
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libblas-dev \
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libbz2-* \
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libcurl4 \
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"libicu[0-9][0-9]" \
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liblapack-dev \
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libpcre2* \
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libjpeg-turbo* \
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libpangocairo-* \
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libpng16* \
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"libreadline${READLINE_VERSION}" \
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libtiff* \
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liblzma* \
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libxt6 \
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make \
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tzdata \
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unzip \
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zip \
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zlib1g
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BUILDDEPS="curl \
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default-jdk \
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devscripts \
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libbz2-dev \
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libcairo2-dev \
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libcurl4-openssl-dev \
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libpango1.0-dev \
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libjpeg-dev \
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libicu-dev \
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libpcre2-dev \
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libpng-dev \
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libreadline-dev \
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libtiff5-dev \
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liblzma-dev \
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libx11-dev \
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libxt-dev \
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perl \
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rsync \
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subversion \
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tcl-dev \
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tk-dev \
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texinfo \
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texlive-extra-utils \
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texlive-fonts-recommended \
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texlive-fonts-extra \
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texlive-latex-recommended \
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texlive-latex-extra \
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x11proto-core-dev \
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xauth \
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xfonts-base \
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xvfb \
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wget \
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zlib1g-dev"
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# shellcheck disable=SC2086
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apt-get install -y --no-install-recommends ${BUILDDEPS}
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## Download R from 0-Cloud CRAN mirror or CRAN
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function download_r_src() {
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wget "https://cloud.r-project.org/src/$1" -O "R.tar.gz" ||
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wget "https://cran.r-project.org/src/$1" -O "R.tar.gz"
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}
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if [ "$R_VERSION" == "devel" ]; then
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download_r_src "base-prerelease/R-devel.tar.gz"
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elif [ "$R_VERSION" == "patched" ]; then
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download_r_src "base-prerelease/R-latest.tar.gz"
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elif [ "$R_VERSION" == "latest" ]; then
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download_r_src "base/R-latest.tar.gz"
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else
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download_r_src "base/R-${R_VERSION%%.*}/R-${R_VERSION}.tar.gz"
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fi
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tar xzf "R.tar.gz"
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cd R-*/
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R_PAPERSIZE=letter \
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R_BATCHSAVE="--no-save --no-restore" \
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R_BROWSER=xdg-open \
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PAGER=/usr/bin/pager \
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PERL=/usr/bin/perl \
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R_UNZIPCMD=/usr/bin/unzip \
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R_ZIPCMD=/usr/bin/zip \
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R_PRINTCMD=/usr/bin/lpr \
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LIBnn=lib \
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AWK=/usr/bin/awk \
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CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \
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CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \
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./configure --enable-R-shlib \
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--enable-memory-profiling \
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--with-readline \
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--with-blas \
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--with-lapack \
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--with-tcltk \
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--with-recommended-packages
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make
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make install
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make clean
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## Add a library directory (for user-installed packages)
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mkdir -p "${R_HOME}/site-library"
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chown root:staff "${R_HOME}/site-library"
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chmod g+ws "${R_HOME}/site-library"
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## Fix library path
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echo "R_LIBS=\${R_LIBS-'${R_HOME}/site-library:${R_HOME}/library'}" >>"${R_HOME}/etc/Renviron.site"
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## Clean up from R source install
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cd ..
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rm -rf /tmp/*
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rm -rf R-*/
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rm -rf "R.tar.gz"
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## Copy the checkbashisms script to local before remove devscripts package.
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## https://github.com/rocker-org/rocker-versioned2/issues/510
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cp /usr/bin/checkbashisms /usr/local/bin/checkbashisms
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# shellcheck disable=SC2086
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if [ "${PURGE_BUILDDEPS}" != "false" ]; then
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apt-get remove --purge -y ${BUILDDEPS}
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fi
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apt-get autoremove -y
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apt-get autoclean -y
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rm -rf /var/lib/apt/lists/*
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# Check the R info
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echo -e "Check the R info...\n"
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R -q -e "sessionInfo()"
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echo -e "\nInstall R from source, done!"

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