diff --git a/Dockerfile b/Dockerfile index ac0f270..9315cbb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # syntax=docker/dockerfile:1 -FROM rocker/rstudio:4.2.1 -MAINTAINER Lee Evans +FROM rocker/rstudio:4.2.3 +LABEL Lee Evans # install OS dependencies including java and python 3 RUN apt-get update && apt-get install -y openjdk-11-jdk liblzma-dev libbz2-dev libncurses5-dev curl python3-dev python3.venv \ @@ -8,7 +8,7 @@ RUN apt-get update && apt-get install -y openjdk-11-jdk liblzma-dev libbz2-dev l && rm -rf /var/lib/apt/lists/* # install utility R packages -RUN install2.r \ +RUN install2.r --error --skipinstalled --repos "https://packagemanager.posit.co/cran/latest" \ openssl \ httr \ xml2 \ @@ -23,9 +23,9 @@ RUN --mount=type=secret,id=build_github_pat \ && cp /tmp/Renviron /usr/local/lib/R/etc/Renviron # install useful R libraries to help RStudio users to create/use their own GitHub Personal Access Token -RUN install2.r \ - usethis \ - gitcreds \ +RUN install2.r --error --skipinstalled --repos "https://packagemanager.posit.co/cran/latest" \ + usethis \ + gitcreds \ && rm -rf /tmp/download_packages/ /tmp/*.rds # create Python virtual environment used by the OHDSI PatientLevelPrediction R package @@ -38,30 +38,23 @@ EOF # install shiny and other R packages used by the OHDSI PatientLevelPrediction R package viewPLP() function # and additional model related R packages -RUN install2.r \ - DT \ - markdown \ - plotly \ - shiny \ - shinycssloaders \ - shinydashboard \ - shinyWidgets \ - xgboost \ +RUN install2.r --error --skipinstalled --repos "https://packagemanager.posit.co/cran/latest" \ + DT \ + markdown \ + plotly \ + shiny \ + shinycssloaders \ + shinydashboard \ + shinyWidgets \ + xgboost \ && rm -rf /tmp/download_packages/ /tmp/*.rds # install the jdbc drivers for database access using the OHDSI DatabaseConnector R package ENV DATABASECONNECTOR_JAR_FOLDER="/opt/hades/jdbc_drivers" -RUN R <