Fixes to non-root user (docker) creation commands and non-root user's permissions

[eitsupi]

Fix #513, Addresses #517

The user creation command has been replaced with the rocker/r-ver one (set default shell, create home dir at once). https://github.com/rocker-org/rocker-versioned2/blob/74e609121d784d54841ec27594e3c3a7f2dc3e1c/scripts/default_user.sh#L10-L12

Also, the site-library permissions have been changed so that the staff group can update as like rocker/r-ver. https://github.com/rocker-org/rocker-versioned2/blob/74e609121d784d54841ec27594e3c3a7f2dc3e1c/scripts/install_R_source.sh#L143-L144

I tried to build and test locally, but got the following error... Perhaps because it is just before the R 4.2.3 release?

#9 10.55 Package r-base-core is not available, but is referred to by another package.
#9 10.55 This may mean that the package is missing, has been obsoleted, or
#9 10.55 is only available from another source
#9 10.55 
#9 10.55 Package r-base is not available, but is referred to by another package.
#9 10.55 This may mean that the package is missing, has been obsoleted, or
#9 10.55 is only available from another source
#9 10.55 However the following packages replace it:
#9 10.55   r-base-core r-doc-info r-doc-html r-base-html
#9 10.55 
#9 10.55 Package r-recommended is not available, but is referred to by another package.
#9 10.55 This may mean that the package is missing, has been obsoleted, or
#9 10.55 is only available from another source
#9 10.55 However the following packages replace it:
#9 10.55   r-cran-mgcv r-cran-survival r-cran-rpart r-base-html r-base-core r-cran-boot
#9 10.55   r-cran-nlme r-cran-lattice r-cran-kernsmooth r-cran-foreign r-cran-cluster
#9 10.55 
#9 10.55 Package r-base-dev is not available, but is referred to by another package.
#9 10.55 This may mean that the package is missing, has been obsoleted, or
#9 10.55 is only available from another source
#9 10.55 
#9 10.56 E: Version '4.2.2-*' for 'r-base' was not found
#9 10.56 E: Version '4.2.2-*' for 'r-base-dev' was not found
#9 10.56 E: Version '4.2.2-*' for 'r-base-core' was not found
#9 10.56 E: Version '4.2.2-*' for 'r-recommended' was not found
------
executor failed running [/bin/sh -c apt-get update         && apt-get install -y --no-install-recommends                 libopenblas0-pthread             littler                 r-cran-docopt                 r-cran-littler     r-base=${R_BASE_VERSION}-*               r-base-dev=${R_BASE_VERSION}-*                 r-base-core=${R_BASE_VERSION}-*            r-recommended=${R_BASE_VERSION}-*       && chown root:staff "/usr/local/lib/R/site-library"     && chmod g+ws "/usr/local/lib/R/site-library"     && ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r      && ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r  && ln -s /usr/lib/R/site-library/littler/examples/installBioc.r /usr/local/bin/installBioc.r      && ln -s /usr/lib/R/site-library/littler/examples/installDeps.r /usr/local/bin/installDeps.r      && ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r  && ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds  && rm -rf /var/lib/apt/lists/*]: exit code: 100

[eddelbuettel]

I am surprised you didn't make the (trivial) fix to the actual current version (and R Core asked for the interim to be made) so commit b238d33 does that now.

[eitsupi]

I am surprised you didn't make the (trivial) fix to the actual current version (and R Core asked for the interim to be made) so commit b238d33 does that now.

Thanks for the follow-up. Actually I have no understanding of how to fix apt package versions......

[eddelbuettel]

Just like the Dockerfile does:

ENV R_BASE_VERSION 4.2.2.20221110

[....]

RUN apt-get update \
        && apt-get install -y --no-install-recommends \
                libopenblas0-pthread \
        littler \
                r-cran-docopt \
                r-cran-littler \
        r-base=${R_BASE_VERSION}-* \
        r-base-dev=${R_BASE_VERSION}-* \
                r-base-core=${R_BASE_VERSION}-* \
        r-recommended=${R_BASE_VERSION}-* \

An =.... argument for the (upstream) version before the hyphen omitting the final build iteration counter that is distro specific.