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|
#!/bin/bash
#
# Provisioner
#
# Parameters
DIRNAME="`dirname $0`"
BASEDIR="$DIRNAME/.."
# Load optional customizations
#
# Search in multiple levels to account when this repository is vendorized.
[ -f "$BASEDIR/.env" ] && source $BASEDIR/.env
[ -f "$BASEDIR/../.env" ] && source $BASEDIR/../.env
[ -f "$BASEDIR/../../.env" ] && source $BASEDIR/../../.env
# Bookdown packaging approach
BOOKDOWN_PACKAGING="${BOOKDOWN_PACKAGING:-DEB}"
# Dependencies
DEPENDENCIES="make"
# LaTeX dependencies
DEPENDENCIES="$DEPENDENCIES texlive-latex-base texlive-latex-recommended texlive-science"
DEPENDENCIES="$DEPENDENCIES texlive-latex-extra texlive-fonts-extra texlive-extra-utils"
DEPENDENCIES="$DEPENDENCIES texlive-xetex texlive-lang-portuguese vim-latexsuite"
# Pandoc dependencies
DEPENDENCIES="$DEPENDENCIES pandoc"
#DEPENDENCIES="$DEPENDENCIES python3-pandocfilters"
# May be unavailable on Debian bookworm onwards
#DEPENDENCIES="$DEPENDENCIES pandoc-citeproc"
# Tufte CSS
# Needed by Tufte HTML output
# https://github.com/jez/pandoc-sidenote
#
# Not available on Debian trixie:
# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1087153
#DEPENDENCIES="$DEPENDENCIES pandoc-sidenote"
#
# Install using cabal instead
#$SUDO apt install cabal-install
#$SUDO cabal update
#$SUDO cabal install pandoc-sidenote
#$SUDO apt install -y libghc-pandoc-sidenote-dev \
# libghc-pandoc-sidenote-doc libghc-pandoc-sidenote-prof
# R dependencies
DEPENDENCIES="$DEPENDENCIES r-cran-rmarkdown r-cran-magick"
# Libraries
DEPENDENCIES="$DEPENDENCIES libpoppler-cpp-dev"
DEPENDENCIES="$DEPENDENCIES libfontconfig1-dev libharfbuzz-dev libfribidi-dev"
DEPENDENCIES="$DEPENDENCIES libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev"
# Fonts
DEPENDENCIES="$DEPENDENCIES fonts-liberation fonts-linuxlibertine"
# Graphviz
DEPENDENCIES="$DEPENDENCIES graphviz"
# Additional BibTeX dependencies
#DEPENDENCIES="$DEPENDENCIES texlive-bibtex-extra"
DEPENDENCIES="$DEPENDENCIES biber pybtex"
# For pdfcrop support
DEPENDENCIES="$DEPENDENCIES texlive-extra-utils"
# Old dependencies
#DEPENDENCIES="$DEPENDENCIES python-yaml python-cheetah python-unidecode python-pycurl python-shortuuid"
#DEPENDNECIES="$DEPENDENCIES python-sphinx python-sphinx-bootstrap-theme python-sphinx-paramlinks"
#DEPENDENCIES="$DEPENDENCIES python-sphinx-patchqueue python-sphinx-rtd-theme python-sphinx-gallery"
#DEPENDENCIES="$DEPENDENCIES python-sphinxcontrib.bibtex-doc"
#DEPENDENCIES="$DEPENDENCIES pelican hugo jekyll"
# Check for sudo
if [ "`whoami`" != "root" ]; then
SUDO="sudo"
fi
# Configure Debian backports
#if which trashman &> /dev/null; then
# trashman install debian-backports
#fi
# Ensure an up-to-date system
$SUDO apt-get update && $SUDO apt-get dist-upgrade -y && \
$SUDO apt-get autoremove -y && $SUDO apt-get clean
# Install dependencies
$SUDO apt install -y $DEPENDENCIES
# Bookdown dependencies
$SUDO apt install -y libcurl4-openssl-dev libssl-dev
if [ "$BOOKDOWN_PACKAGING" == "CRAN" ]; then
$SUDO $DIRNAME/provision.R
else
$SUDO apt install -y r-cran-bookdown
$SUDO apt install -y r-cran-pdftools
# As of 2024-08-16, this package is not available on Debian bookworm
#$SUDO Rscript -e 'install.packages("eulerr")'
# As of 2024-08-16, ggplot2 from Debian bookworm version is 3.4.1, whereas
# some downstreams need functionality from 3.5.0 (specifically, the ability
# to use 'theme(legend.position = "inside"' constructs.
#
# The workaround was to install ggplot2 version from CRAN.
#
# This issue was fixed with Debian trixie, so ggplot2 is not needed anymore
# as of 2026-01-31 (it was removed from the test environment using the
# following command:
#
# sudo Rscript -e 'remove.packages("ggplot2")'
#
# In fact, using ggplot2 from CRAN with the other packages from Debian
# leads to this error:
#
# > library(ggplot2)
# > ggplot(mpg, aes(displ, hwy, colour = class)) + geom_point()
# Error in ggplot(mpg, aes(displ, hwy, colour = class)) + geom_point() :
# non-numeric argument to binary operator
# In addition: Warning message:
# Incompatible methods ("Ops.S7_object", "+.gg") for "+"
#
#$SUDO Rscript -e 'install.packages("ggplot2")'
fi
|
