added dockerfile; updated renv

.Rprofile

@@ -1 +1,5 @@
+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")

Dockerfile

@@ -0,0 +1,18 @@
+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