Fix the fuse-workspace.jar file permissions.

Dockerfile

@@ -5,7 +5,69 @@ 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 required by vlab5 VRE https://support.d4science.org/issues/23536
+
+ENV DEBIAN_FRONTEND noninteractive
+# Upgrade, install some R dependencies and base python3
+# Add libcurl4-gnutls-dev and remove libcurl4-openssl-dev because
+# 
+# libraptor2-dev : Depends: libcurl4-gnutls-dev but it is not installable
+RUN apt-get update --yes && \
+    apt-get install --yes --no-install-recommends \
+    libgdal-dev \
+    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 \
+    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 \
+    libcurl4-gnutls-dev \
+    libsodium-dev \
+    libudunits2-dev \
+    libglpk40
+
+RUN mkdir -p /opt/workspace-lib
+RUN mkdir /var/log/workspace-lib
+ADD https://maven.d4science.org/nexus/content/repositories/gcube-snapshots/org/gcube/data-access/sh-fuse-integration/2.0.0-SNAPSHOT/sh-fuse-integration-2.0.0-20211005.090627-1-jar-with-dependencies.jar /opt/workspace-lib/fuse-workspace.jar
+RUN chmod 0644 /opt/workspace-lib/fuse-workspace.jar
+
+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*
+

Jenkinsfile-fisheriesatlas-vlab5

@@ -9,15 +9,17 @@ pipeline {
       label 'docker'
   }
   environment {
-    imagename = "d4science/rstudio-d4science"
-    registryCredential = 'e348bfab-5580-4db6-b0e0-d854966bde08'
+    imagename = "rstudio/rstudio-fisheriesatlas-vlab5"
+    hubname = "hub.dev.d4science.org"
+    registryUrl = "https://hub.dev.d4science.org"
+    registryCredential = 'cccd3cf5-9d6c-4044-85d6-59bede0c43f4'
     dockerImage = ''
     git_url='https://code-repo.d4science.org/gCubeSystem/rstudio-d4science.git'
   }
   stages {
     // stage('Cloning Git') {
     //   steps {
-    //     git([url: git_url, branch: '2023-03-R4-2', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346'])
+    //     git([url: git_url, branch: 'fisheriesatlas-vlab5', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346'])
     //   }
     // }
     stage('Building image') {
@@ -30,17 +32,17 @@ pipeline {
     stage('Deploy Image') {
       steps{
         script {
-          docker.withRegistry( '', registryCredential ) {
+          docker.withRegistry( registryUrl, registryCredential ) {
             dockerImage.push("$BUILD_NUMBER")
-            dockerImage.push('2023-03-R4-2')
+            dockerImage.push('latest')
           }
         }
       }
     }
     stage('Remove Unused docker image') {
       steps{
-        sh "docker rmi $imagename:$BUILD_NUMBER"
-        sh "docker rmi $imagename:2023-03-R4-2"
+        sh "docker rmi $hubname/$imagename:$BUILD_NUMBER"
+        sh "docker rmi $hubname/$imagename:latest"
 
       }
     }

README.md

@@ -1,6 +1,6 @@
 # rstudio-d4science
 
-Rstudio image that builds from "r-full"
+Rstudio image that builds from "d4science/rstudio-base:2023-03-R4-2"
+
+This is the version customized for vfisheriesatlas-vlab5, see https://support.d4science.org/issues/23536
 
-One branch for each corresponding *major.minor* `R` version and for each
-customization on top of the R version.

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