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added dockerfile; updated renv
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f-kretschmer committed Feb 15, 2024
1 parent cb6d543 commit 4b729b6
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4 changes: 4 additions & 0 deletions .Rprofile
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options(renv.config.ppm.enabled = TRUE)
options(renv.config.ppm.default = TRUE)
options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/bookworm/2024-02-06"))
options(renv.config.repos.override = getOption("repos"))
source("renv/activate.R")
18 changes: 18 additions & 0 deletions Dockerfile
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FROM debian:12
# install python deps
RUN apt-get update && apt-get install -y python3-pip python3-venv \
python3-pandas python3-requests python3-zeep python3-tabulate python3-sklearn python3-yaml
RUN pip install --break-system-packages pubchempy # not available as debian package
# install R + R deps
RUN apt-get update && apt-get install -y r-base r-base-dev \
# dependencies necessary for some R packages
libcurl4-openssl-dev libssl-dev default-jdk libgit2-dev
COPY renv.lock renv.lock
COPY renv renv
COPY .Rprofile .Rprofile
RUN R CMD javareconf # configure Java for rJava
RUN R -e "renv::restore()"
# NOTE: uncomment the next line to create updated renv.lock file
# RUN R -e "renv::snapshot()"
# install dependencies for GitHub workflow
RUN apt-get update && apt-get install -y git git-lfs bash unzip curl
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