Do not install R packages from github.
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@ -45,14 +45,15 @@ 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 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 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 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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#RUN mv -f /etc/R/Renviron.site.1 /etc/R/Renviron.site
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#RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest DanOvando/sraplus ; done
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# Ensure that we remove the source packages
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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 rm -fr /tmp/downloaded_packages/*
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