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remove custom definition of R_LIBS in scripts/install_R_source.sh #866

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remove custom definition of R_LIBS in scripts/install_R_source.sh #866

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3 changes: 0 additions & 3 deletions scripts/install_R_source.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -145,9 +145,6 @@ 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"
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Sorry I haven't caught up with the discussion, but do we need to remove this instead of changing the order?

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I also fear (based on mere eyeballing) that the current definition may be quite right. It's not easy to get this right for all cases. I also think R prefers use of R_LIBS_SITE. In Renviron (for the Debian package) I now set

# edd Apr 2003  Allow local install in /usr/local, also add a directory for
#               Debian packaged CRAN packages, and finally the default dir
# edd Jul 2007  Now use R_LIBS_SITE, not R_LIBS
# edd Jan 2023  Modify R_LIBS_{USER,SITE} respecting existing values (cf discussion with Kurt Hornik)
R_LIBS_USER=${R_LIBS_USER:-'%U'}
R_LIBS_SITE=${R_LIBS_SITE:-'/usr/local/lib/R/site-library:%S'}

and there also is this in Renviron.site

## # We comment out this line in the default Renviron, you can re-enable it here
## # @R_PLATFORM@ can be eg x86_64-pc-linux-gnu, see /etc/R/Renviron for R_PLATFORM
## # @MAJ_MIN_VERSION@ is likely something like '3.4', see /etc/R/Renviron too
## #
## # Also note that you set this per-user via '%p' and '%v' for platform and version
#R_LIBS_USER=${R_LIBS_USER-'~/R/@R_PLATFORM@-library/@MAJ_MIN_VERSION@'}

as well as this possible interacting with what I have above:

## edd Apr 2003  Allow local install in /usr/local, also add a directory for
##               Debian packaged CRAN packages, and finally the default dir
## edd Jul 2007  Now use R_LIBS_SITE, not R_LIBS
## edd Mar 2022  Now in Renviron.site reflecting R_LIBS_SITE
R_LIBS_SITE="/usr/local/lib/R/site-library/:${R_LIBS_SITE}:/usr/lib/R/library"

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I am not sure where does that leave us with regards to this PR: Do we agree or disagree to remove the R_LIBS definition as proposed by this PR ?

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Based on my testing using R 4.4.2, changing this line from using R_LIBS to R_LIBS_SITE will also resolve the issue of the user's library path being set last:

echo "R_LIBS_SITE=\${R_LIBS_SITE:-'${R_HOME}/site-library:${R_HOME}/library'}" >> "${R_HOME}/etc/Renviron.site"

After that change, the user's library path will always be set first.


## Clean up from R source install
cd ..
rm -rf /tmp/*
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