Merge pull request #56 from nmfs-opensci/eeholmes-patch-1

install apt packages after R installation

Author: eeholmes

appendix

@@ -1,6 +1,21 @@
+USER root
+
+# Install R, RStudio via Rocker scripts
+ENV R_VERSION="4.4.1"
+ENV R_DOCKERFILE="verse_${R_VERSION}"
+RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
+  chmod +x ${REPO_DIR}/rocker.sh && \
+  ${REPO_DIR}/rocker.sh
+
+# Install extra cmd line packages after R installation
+RUN apt-get update && \
+  xargs -a ${REPO_DIR}/apt-extras.txt apt-get install --yes --no-install-recommends && \
+  apt-get autoremove --purge && \
+  apt-get clean && \
+  rm -rf /var/lib/apt/lists/*
+
 # Re-enable man pages disabled in Ubuntu 18 minimal image
 # https://wiki.ubuntu.com/Minimal
-USER root
 RUN yes | unminimize
 # NOTE: $NB_PYTHON_PREFIX is the same as $CONDA_PREFIX at run-time.
 # $CONDA_PREFIX isn't available in this context.
@@ -9,11 +24,5 @@ RUN yes | unminimize
 ENV MANPATH="${NB_PYTHON_PREFIX}/share/man:${MANPATH}"
 RUN mandb
 
-ENV R_VERSION="4.4.1"
-ENV R_DOCKERFILE="verse_${R_VERSION}"
-RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
-  chmod +x ${REPO_DIR}/rocker.sh && \
-  ${REPO_DIR}/rocker.sh
-
 # Revert to default user
 USER ${NB_USER}

apt-extras.txt

@@ -37,18 +37,10 @@ gfortran
 
 # Dependencies for nbconvert and myst
 # LaTeX tools
-texlive-xetex
-texlive-plain-generic
-texlive-fonts-extra
-texlive-fonts-recommended
-texlive-lang-chinese
-texlive-science
-latexmk
-lmodern
-latexdiff
+# Are installed by R installation
 
 # Other useful document-related tools
-pandoc
+# pandoc installed by R installation
 imagemagick
 # /end nbconvert/myst tools
 
@@ -68,21 +60,14 @@ tig  # console UI for git
 multitail
 tree
 
-# For later, these are not available in 18.04
-#browsh # text-based web browser, occasionally handy
-#dasel  # json/yml/csv/etc data wrangling at the terminal
-#fzf   # fuzzy file finder
-
-## This section adds tools for desktop environment usage
+## This section adds tools needed for desktop environment
 dbus-x11
 xorg
 xubuntu-icon-theme
 xfce4
 xfce4-goodies
 xclip
 xsel
-firefox
-chromium-browser
 
 # GUI text editors
 emacs

postBuild

@@ -1,12 +1,6 @@
 #!/bin/bash -l
 set -euo pipefail
 
-apt-get update && \
-  xargs -a apt-extras.txt apt-get install --yes --no-install-recommends && \
-  apt-get autoremove --purge && \
-  apt-get clean && \
-  rm -rf /var/lib/apt/lists/*
-
 # Put our custom Jupyter Server config into appropriate platform
 # This path is determined by looking at output of `jupyter --path` in the hub
 # We copy both to notebook server config and jupyter server config, because either can be