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feat: make arrow installation stable for Armadillo dsBase package #23

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3 changes: 0 additions & 3 deletions azure-pipelines.yml
Original file line number Diff line number Diff line change
@@ -1,6 +1,3 @@
trigger:
- main

pr:
- main

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40 changes: 28 additions & 12 deletions production/armadillo-rserver/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -2,29 +2,45 @@ FROM rocker/r-ver:4.1.1

ENV DEBUG FALSE

# Copy script to install deps
COPY scripts/install-arrow.bash /

# Install dependencies of OS to use RServe
RUN apt-get update -qq && apt-get -y --no-install-recommends install \
libssl-dev net-tools procps lsof libcurl4-openssl-dev git
RUN apt update -qq
RUN apt -y --no-install-recommends install \
libssl-dev \
net-tools \
procps \
lsof \
libcurl4-openssl-dev \
git \
cmake \
wget \
ca-certificates \
lsb-release

# Install some debug packages needed by armadillo to retrieve list of R processes
RUN install2.r --error remotes ps --repos "https://cloud.r-project.org/"

# Install up-to-date version of apache arrow
# install arrow to be able to transfer files from file storage to R-environment
# the base image is windows WSL2 image with Ubuntu Focal installed as base layer
# IMPORTANT: "focal" needs to change if you upgrade to a newer Ubuntu base layer
ENV ARROW_VERSION "5.0.0"
RUN ./install-arrow.bash
RUN R -e "source('https://raw.githubusercontent.com/apache/arrow/release-${ARROW_VERSION}/r/R/install-arrow.R'); install_arrow();"
RUN wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/pool/focal/main/a/apache-arrow-apt-source/apache-arrow-apt-source_${ARROW_VERSION}-1_all.deb
RUN apt install -y ./apache-arrow-apt-source_${ARROW_VERSION}-1_all.deb
ENV LIBARROW_MINIMAL FALSE
RUN installGithub.r "apache/arrow/r@apache-arrow-${ARROW_VERSION}"

# Install some debug packages needed by armadillo to retrieve list of R processes
RUN install2.r --error remotes ps dplyr magrittr --repos "https://cloud.r-project.org/"
RUN apt update -qq
RUN apt install -y \
libparquet-dev \
libparquet-glib-dev

# Install RServer
ENV RSERVER_VERSION "0.1.2"
RUN install2.r --error "https://registry.molgenis.org/repository/r-hosted/src/contrib/MolgenisRserve_${RSERVER_VERSION}.tar.gz" --repos NULL

# Install dsBase package
ENV DSBASE_VERSION "6.1.0"
ENV DS_PKG_VERSION "6.1.0"
RUN install2.r --error RANN stringr lme4 ggplot2 reshape2 --repos "https://cloud.r-project.org/"
RUN installGithub.r "datashield/dsBase@${DSBASE_VERSION}"
RUN installGithub.r "datashield/dsBase@${DS_PKG_VERSION}"

# Startup the RServer
CMD R -e "MolgenisRserve::Rserve(debug=${DEBUG}, args='--vanilla --RS-set remote=enable --RS-set auth=disable --RS-set daemon=disable')"
3 changes: 1 addition & 2 deletions production/armadillo-rserver/README.md
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Expand Up @@ -3,9 +3,8 @@ The RServer for DataSHIELD has installed collections of tools to support DataSHI

## Contents
There are several DataSHIELD related dependencies installed
- [RServer](https://github.com/molgenis/Rserve/releases/tag/v0.1.2)=0.1.2
- [RServer](https://github.com/molgenis/Rserve/releases/tag/v0.1.2)
- [dsBase](https://github.com/datashield/dsBase)
- [resourcer](https://github.com/obiba/resourcer)

## Usage
There are several platforms on which you can run RServer.
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2 changes: 1 addition & 1 deletion production/armadillo-rserver/package.json
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "@datashield/armadillo-rserver",
"version": "1.0.0",
"version": "6.1.0",
"license": "LGPL-3.0",
"description": "Armadillo RServe 0.1.2 with dsBase 6.x",
"repository": {
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42 changes: 0 additions & 42 deletions production/armadillo-rserver/scripts/install-arrow.bash

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