Merge pull request #30 from nmfs-opensci/eeholmes-dev2-1

Eeholmes dev2 1

.github/workflows/build-dev.yaml

@@ -4,15 +4,15 @@ on:
   workflow_dispatch: null
   push:
     branches:
-      - dev
+      - dev2
     paths:
       - 'apt.txt'
       - 'environment.yml'
       - 'start'
       - 'postBuild'
       - 'appendix'
       - 'rocker.sh'
-      - '.github/workflows/build.yaml'
+      - '.github/workflows/build-dev.yaml'
 
 jobs:
   build-and-push:

appendix

@@ -9,7 +9,12 @@ RUN yes | unminimize
 ENV MANPATH="${NB_PYTHON_PREFIX}/share/man:${MANPATH}"
 RUN mandb
 
-RUN chmod +x ${REPO_DIR}/rocker.sh && ${REPO_DIR}/rocker.sh
+ENV R_VERSION="4.4.1"
+ENV R_HOME="/usr/local/lib/R"
+ENV TZ="Etc/UTC"
+
+COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
+RUN /rocker_scripts/install_R_source.sh
 
 # Revert to default user
 USER ${NB_USER}

scripts/install_R_source.sh

@@ -0,0 +1,174 @@
+#!/bin/bash
+
+## Install R from source.
+##
+## In order of preference, first argument of the script, the R_VERSION variable.
+## ex. latest, devel, patched, 4.0.0
+##
+## 'devel' means the prerelease development version (Latest daily snapshot of development version).
+## 'patched' means the prerelease patched version (Latest daily snapshot of patched version).
+
+set -e
+
+R_VERSION=${1:-${R_VERSION:-"latest"}}
+PURGE_BUILDDEPS=${PURGE_BUILDDEPS:-"true"}
+
+# shellcheck source=/dev/null
+source /etc/os-release
+
+apt-get update
+apt-get -y install locales
+
+## Configure default locale
+LANG=${LANG:-"en_US.UTF-8"}
+/usr/sbin/locale-gen --lang "${LANG}"
+/usr/sbin/update-locale --reset LANG="${LANG}"
+
+export DEBIAN_FRONTEND=noninteractive
+
+R_HOME=${R_HOME:-"/usr/local/lib/R"}
+
+READLINE_VERSION=8
+if [ "${UBUNTU_CODENAME}" == "bionic" ]; then
+    READLINE_VERSION=7
+fi
+
+apt-get install -y --no-install-recommends \
+    bash-completion \
+    ca-certificates \
+    file \
+    fonts-texgyre \
+    g++ \
+    gfortran \
+    gsfonts \
+    libblas-dev \
+    libbz2-* \
+    libcurl4 \
+    "libicu[0-9][0-9]" \
+    liblapack-dev \
+    libpcre2* \
+    libjpeg-turbo* \
+    libpangocairo-* \
+    libpng16* \
+    "libreadline${READLINE_VERSION}" \
+    libtiff* \
+    liblzma* \
+    libxt6 \
+    make \
+    tzdata \
+    unzip \
+    zip \
+    zlib1g
+
+BUILDDEPS="curl \
+    default-jdk \
+    devscripts \
+    libbz2-dev \
+    libcairo2-dev \
+    libcurl4-openssl-dev \
+    libpango1.0-dev \
+    libjpeg-dev \
+    libicu-dev \
+    libpcre2-dev \
+    libpng-dev \
+    libreadline-dev \
+    libtiff5-dev \
+    liblzma-dev \
+    libx11-dev \
+    libxt-dev \
+    perl \
+    rsync \
+    subversion \
+    tcl-dev \
+    tk-dev \
+    texinfo \
+    texlive-extra-utils \
+    texlive-fonts-recommended \
+    texlive-fonts-extra \
+    texlive-latex-recommended \
+    texlive-latex-extra \
+    x11proto-core-dev \
+    xauth \
+    xfonts-base \
+    xvfb \
+    wget \
+    zlib1g-dev"
+
+# shellcheck disable=SC2086
+apt-get install -y --no-install-recommends ${BUILDDEPS}
+
+## Download R from 0-Cloud CRAN mirror or CRAN
+function download_r_src() {
+    wget "https://cloud.r-project.org/src/$1" -O "R.tar.gz" ||
+        wget "https://cran.r-project.org/src/$1" -O "R.tar.gz"
+}
+
+if [ "$R_VERSION" == "devel" ]; then
+    download_r_src "base-prerelease/R-devel.tar.gz"
+elif [ "$R_VERSION" == "patched" ]; then
+    download_r_src "base-prerelease/R-latest.tar.gz"
+elif [ "$R_VERSION" == "latest" ]; then
+    download_r_src "base/R-latest.tar.gz"
+else
+    download_r_src "base/R-${R_VERSION%%.*}/R-${R_VERSION}.tar.gz"
+fi
+
+tar xzf "R.tar.gz"
+cd R-*/
+
+R_PAPERSIZE=letter \
+    R_BATCHSAVE="--no-save --no-restore" \
+    R_BROWSER=xdg-open \
+    PAGER=/usr/bin/pager \
+    PERL=/usr/bin/perl \
+    R_UNZIPCMD=/usr/bin/unzip \
+    R_ZIPCMD=/usr/bin/zip \
+    R_PRINTCMD=/usr/bin/lpr \
+    LIBnn=lib \
+    AWK=/usr/bin/awk \
+    CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \
+    CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \
+    ./configure --enable-R-shlib \
+    --enable-memory-profiling \
+    --with-readline \
+    --with-blas \
+    --with-lapack \
+    --with-tcltk \
+    --with-recommended-packages
+
+make
+make install
+make clean
+
+## Add a library directory (for user-installed packages)
+mkdir -p "${R_HOME}/site-library"
+chown root:staff "${R_HOME}/site-library"
+chmod g+ws "${R_HOME}/site-library"
+
+## Fix library path
+echo "R_LIBS=\${R_LIBS-'${R_HOME}/site-library:${R_HOME}/library'}" >>"${R_HOME}/etc/Renviron.site"
+
+## Clean up from R source install
+cd ..
+rm -rf /tmp/*
+rm -rf R-*/
+rm -rf "R.tar.gz"
+
+## Copy the checkbashisms script to local before remove devscripts package.
+## https://github.com/rocker-org/rocker-versioned2/issues/510
+cp /usr/bin/checkbashisms /usr/local/bin/checkbashisms
+
+# shellcheck disable=SC2086
+if [ "${PURGE_BUILDDEPS}" != "false" ]; then
+    apt-get remove --purge -y ${BUILDDEPS}
+fi
+apt-get autoremove -y
+apt-get autoclean -y
+rm -rf /var/lib/apt/lists/*
+
+# Check the R info
+echo -e "Check the R info...\n"
+
+R -q -e "sessionInfo()"
+
+echo -e "\nInstall R from source, done!"