feat: upgrade to dsBase 6.2.0

azure-pipelines.yml

@@ -1,6 +1,3 @@
-trigger:
-- main
-
 pr:
 - main
 

production/armadillo-rserver-survival/Dockerfile

@@ -0,0 +1,10 @@
+FROM datashield/armadillo-rserver:6.1
+
+# Install surival dependency
+RUN install2.r --error "survival"
+
+# Install dsSurvival package
+ENV DS_PKG_VERSION "v1.0.0"
+RUN installGithub.r "neelsoumya/dsSurvival@${DS_PKG_VERSION}"
+
+CMD R -e "MolgenisRserve::Rserve(debug=${DEBUG}, args='--vanilla --RS-set remote=enable --RS-set auth=disable --RS-set daemon=disable')"

production/armadillo-rserver/Dockerfile

@@ -1,30 +1,48 @@
 FROM rocker/r-ver:4.1.1
+# R versions larger then 4.1.1 break the armadillo backend 
+# R-options won't load anymore
 
 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"
-RUN install2.r --error RANN stringr lme4 ggplot2 reshape2 --repos "https://cloud.r-project.org/"
-RUN installGithub.r "datashield/dsBase@${DSBASE_VERSION}"
+ENV DS_PKG_VERSION "6.2.0"
+RUN install2.r --error RANN stringr lme4 ggplot2 reshape2 polycor splines --repos "https://cloud.r-project.org/"
+RUN installGithub.r "datashield/dsBase@${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')"

production/armadillo-rserver/README.md

@@ -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.

production/armadillo-rserver/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@datashield/armadillo-rserver",
-  "version": "1.0.0",
+  "version": "6.2.0",
   "license": "LGPL-3.0",
   "description": "Armadillo RServe 0.1.2 with dsBase 6.x",
   "repository": {