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add bspm for package installation #122

@eeholmes

Description

@eeholmes
  • test in repo2docker. doesn't seem to actually work
  • how can user turn this off?
  • install in docker file
  • Check all the ENVs are properly exported to child docker builds
  • Test with install.R install.package("sf", "terra", "TMB", "av")

Install bspm

## Fifth: install bspm (and its Python requirements) and enable it
## If needed (in bare container, say) install python tools for bspm and R itself
apt-get install --yes --no-install-recommends python3-{dbus,gi,apt} \
	make sudo r-cran-{docopt,littler,remotes} 
## Then install bspm (as root) and enable it, and enable a speed optimization
Rscript -e 'install.packages("bspm")'
R_HOME=$(R RHOME)
# must go first
echo "options(bspm.sudo = TRUE)" >> ${R_HOME}/etc/Rprofile.site
echo "options(bspm.version.check=FALSE)" >> ${R_HOME}/etc/Rprofile.site
echo "suppressMessages(bspm::enable())" >> ${HOME}/.Rprofile

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