From 5843c8d994f41f21e4c2dfa4748bcd7608a32e5e Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>
Date: Tue, 16 Apr 2024 20:01:36 +0200
Subject: [PATCH] Branch for the fisheriatlas-vlab5 rstudio

---
 Dockerfile                                    | 56 ++++++++++++++++---
 ...system => Jenkinsfile-fisheriesatlas-vlab5 |  4 +-
 README.md                                     |  2 +-
 install2r-packages.txt                        | 20 +++++++
 wb3-install2r-packages.txt                    | 28 ----------
 5 files changed, 72 insertions(+), 38 deletions(-)
 rename Jenkinsfile-wb3-ecosystem => Jenkinsfile-fisheriesatlas-vlab5 (91%)
 create mode 100644 install2r-packages.txt
 delete mode 100644 wb3-install2r-packages.txt

diff --git a/Dockerfile b/Dockerfile
index ab740ab..d27073e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -5,17 +5,59 @@ LABEL org.d4science.image.licenses="EUPL-1.2" \
       org.d4science.image.vendor="D4Science <https://www.d4science.org>" \
       org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>"
 
-# R and python3 packages required by wb3 ecosystem https://support.d4science.org/issues/26459
-COPY wb3-install2r-packages.txt /rocker_scripts
-RUN for f in `cat //rocker_scripts/wb3-install2r-packages.txt` ; do install2.r --error --skipinstalled --ncpus -1 $f || exit 1 ; done
+# R required by vlab5 VRE https://support.d4science.org/issues/23536
 
-RUN pip3 install \
-    numpy \
-    mbtr \
-    pandas
+ENV DEBIAN_FRONTEND noninteractive
+# Upgrade, install some R dependencies and base python3
+RUN apt-get update --yes && \
+    apt-get dist-upgrade --yes && \
+    apt-get install --yes --no-install-recommends \
+    libgdal-devel \
+    pandoc \
+    pandoc-citeproc \
+    texlive-xetex \
+    texlive-latex-base \
+    texlive-latex-recommended \
+    texlive-fonts-recommended \
+    texlive-fonts-extra \
+    texlive-formats-extra \
+    libssl-dev \
+    libxml2-dev \
+    libv8-dev \
+    libsecret-1-dev \
+    librdf0-dev \
+    libcurl4-openssl-dev \
+    libgit2-dev \
+    libxslt-dev \
+    librdf0 \
+    redland-utils \
+    rasqal-utils \
+    raptor2-utils \
+    libcairo2-dev \
+    libpoppler-cpp-dev \
+    libmagick++-dev \
+    cmake \
+    cargo \
+    libavfilter-dev \
+    libjq-dev \
+    libprotobuf-dev \
+    protobuf-compiler \
+    libproj-dev
+
+COPY install2r-packages.txt /rocker_scripts
+RUN for f in `cat //rocker_scripts/install2r-packages.txt` ; do install2.r --error --skipinstalled --ncpus -1 $f || exit 1 ; done
+
+RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/jammy/latest r-geoflow/geoflow
+RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/jammy/latest hrbrmstr/streamgraph
 
 # Rstudio settings
 COPY rsession.conf /etc/rstudio/rsession.conf
 RUN chmod 0644 /etc/rstudio/rsession.conf
 RUN curl -o "${R_HOME}/etc/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"
 
+RUN rm -fr /tmp/downloaded_packages/*
+
+RUN rm -fr /tmp/downloaded_packages/* && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* && \
+    rm -f /tmp/R*
+
diff --git a/Jenkinsfile-wb3-ecosystem b/Jenkinsfile-fisheriesatlas-vlab5
similarity index 91%
rename from Jenkinsfile-wb3-ecosystem
rename to Jenkinsfile-fisheriesatlas-vlab5
index d947ae4..16f58c2 100644
--- a/Jenkinsfile-wb3-ecosystem
+++ b/Jenkinsfile-fisheriesatlas-vlab5
@@ -9,7 +9,7 @@ pipeline {
       label 'docker'
   }
   environment {
-    imagename = "rstudio/rstudio-wb3-ecosystem"
+    imagename = "rstudio/rstudio-fisheriesatlas-vlab5"
     hubname = "hub.dev.d4science.org"
     registryUrl = "https://hub.dev.d4science.org"
     registryCredential = 'cccd3cf5-9d6c-4044-85d6-59bede0c43f4'
@@ -19,7 +19,7 @@ pipeline {
   stages {
     // stage('Cloning Git') {
     //   steps {
-    //     git([url: git_url, branch: 'wb3-ecosystem', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346'])
+    //     git([url: git_url, branch: 'fisheriesatlas-vlab5', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346'])
     //   }
     // }
     stage('Building image') {
diff --git a/README.md b/README.md
index 772b8f1..f742eea 100644
--- a/README.md
+++ b/README.md
@@ -2,5 +2,5 @@
 
 Rstudio image that builds from "d4science/rstudio-base:2023-03-R4-2"
 
-This is the version customized for WB3 ecosystem, see https://support.d4science.org/issues/26459
+This is the version customized for vfisheriesatlas-vlab5, see https://support.d4science.org/issues/23536
 
diff --git a/install2r-packages.txt b/install2r-packages.txt
new file mode 100644
index 0000000..7bf14f2
--- /dev/null
+++ b/install2r-packages.txt
@@ -0,0 +1,20 @@
+remotes
+dotenv
+here
+magick
+pbdZMQ
+nloptr
+tinytex
+rpostgis
+gargle
+googledrive
+gsheet
+renv
+shinyWidgets
+leaflet
+leaflet.extras
+leaflet.minicharts
+leafpm
+mapedit
+xml2
+pals
diff --git a/wb3-install2r-packages.txt b/wb3-install2r-packages.txt
deleted file mode 100644
index a06c09b..0000000
--- a/wb3-install2r-packages.txt
+++ /dev/null
@@ -1,28 +0,0 @@
-abind
-caret
-corrplot
-devtools
-dendextend
-ncdf4
-parallel
-pdftools
-rgbif
-reticulate
-tidyverse
-tidymodels
-raster
-DALEX
-DALEXtra
-xgboost
-RSQLite
-feather
-vroom
-virtualspecies
-usdm
-robis
-RColorBrewer
-fields
-pastecs
-ecospat
-mvrsquared
-bestNormalize