/etc/R must be created.
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Dockerfile
10
Dockerfile
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@ -27,7 +27,8 @@ RUN apt-get update && apt-get install -y \
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proj-bin \
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proj-bin \
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proj-data \
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proj-data \
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libgsl23 \
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libgsl23 \
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postgresql-server-dev-all
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postgresql-server-dev-all \
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libsecret-1-0
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# Install the R packages we need, using the binary distribution
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# Install the R packages we need, using the binary distribution
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# at https://packagemanager.rstudio.com/client/#/repos/1/overview
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# at https://packagemanager.rstudio.com/client/#/repos/1/overview
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@ -44,12 +45,17 @@ RUN for l in `cat /tmp/r_non_cran_pkgs.txt` ; do \
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# From github
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# From github
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ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_github_pkgs.txt /tmp
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ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_github_pkgs.txt /tmp
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RUN mkdir -p /etc/R
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RUN echo "GITHUB_PAT=$GITHUB_PAT" >> /etc/R/Renviron.site
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RUN echo "GITHUB_PAT=$GITHUB_PAT" >> /etc/R/Renviron.site
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#RUN for g in `cat /tmp/r_github_pkgs.txt` ; do \
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#RUN for g in `cat /tmp/r_github_pkgs.txt` ; do \
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# Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
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# Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
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# -e " require(devtools); devtools::install_github('$g')" ; done
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# -e " require(devtools); devtools::install_github('$g')" ; done
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RUN export GITHUB_PAT ; for g in `cat /tmp/r_github_pkgs.txt` ; do installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest $g ; done
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RUN export GITHUB_PAT ; for g in `cat /tmp/r_github_pkgs.txt` ; do installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest $g ; done
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RUN grep -v "GITHUB_PATH" /etc/R/Renviron.site > /etc/R/Renviron.site.1
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RUN mv -f /etc/R/Renviron.site.1 /etc/R/Renviron.site
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# Ensure that we remove the source packages
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RUN rm -fr /tmp/downloaded_packages/*
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RUN /rocker_scripts/install_rstudio.sh
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RUN /rocker_scripts/install_rstudio.sh
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RUN /rocker_scripts/install_pandoc.sh
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RUN /rocker_scripts/install_pandoc.sh
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