Updating to RStudio 2023

lang/RStudio/README.md

@@ -1,43 +1,54 @@
 # RStudio
 
-RStudio is an Integrated Development Environment (IDE) for the R language. By containerizing RStudio, a scientist can leverage the reproducibility and portability of the Singularity platform, allowing them to build data visualizations and analysis tools and ensure that they behave exactly the same in a new environment. 
+RStudio is an Integrated Development Environment (IDE) for the R language. By containerizing RStudio, a scientist can leverage the reproducibility and portability of the Singularity platform, allowing them to build data visualizations and analysis tools and ensure that they behave exactly the same in a new environment.
 
 The definiton file affords some flexibility, allowing you to run RStudio several different ways:
 
-## Instance:
+## Instance
+
  This will start up rstudio-server, on default port of 8787
 
-```$ singularity instance start rstudio.sif rs```
+```bash
+singularity instance start \
+  --bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server \
+  RStudio.sif rs --server-user=$(whoami) --www-address=0.0.0.0
+```
+
+## Run
 
-## Run:
  This will run rstudio IDE
 
-```$ singularity run rstudio.sif```
+```bash
+singularity run rstudio.sif
+```
+
+## Exec
 
-## Exec:
  Any program in the container, but specifically for running R directly.
 
-```$ singularity exec rstudio.sif R -f myfile.r```
+```bash
+singularity exec rstudio.sif R -f myfile.r
+```
 
 To build the image run:
 
-```$ sudo singularity build rstudio.sif RStudio.def```
+```bash
+sudo singularity build rstudio.sif RStudio.def
+```
 
 When you use run for the IDE, you may need to execute it like:
 
+```bash
+SINGULARITYENV_DISPLAY=${DISPLAY} \
+  singularity run rstudio.sif
+```
 
-```$ SINGULARITYENV_DISPLAY=${DISPLAY} \
-  singularity run rstudio.sif```
-
-This is needed only if the `DISPLAY` environment variable does not automatically propagate from your host environment to the container.
+For a modification of rstudio-server, for example to run on port 9999:
 
-For a modification of rstudio-server, you can create a `rstudio.conf` file, and bind mount it into the container. For example to run on port 9999:
-
-
-```$ echo "www-port=9999" > rserver.conf
-$ singularity instance start \
-  -B rserver.conf:/etc/rstudio/rserver.conf \
-  rstudio.sif rs```
+```bash
+singularity instance start \
+  --bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server \
+  RStudio.sif rs --server-user=$(whoami) --www-address=0.0.0.0 --www-port=9999
+```
 
 You will then access your rstudio-server instance at:  [http://localhost:9999](http://localhost:9999)
-

lang/RStudio/RStudio.def

@@ -1,21 +1,35 @@
 Bootstrap: library
-From: debian:9
+From: ubuntu:22.04
 
 %environment
-    LC_ALL="C"
+    LANG=en_US.UTF-8    
+    LC_ALL="en_US.UTF-8"
+    export LANG
     export LC_ALL
 
 %post
-    apt-get update
-    apt-get -y install systemd systemd-sysv gdebi-core procps libssl1.1 ed wget curl libqt5webkit5 libqt5core5a
-    apt-get -y install r-base r-base-dev
+    export DEBIAN_FRONTEND=noninteractive
+    export TZ=Etc/UTC
+    apt update -qq
+    apt install -y --no-install-recommends software-properties-common dirmngr wget locales
 
-    curl https://download1.rstudio.org/rstudio-xenial-1.1.456-amd64.deb > /rstudio-1.1.456-amd64.deb
-    apt-get -y install /rstudio-1.1.456-amd64.deb
+    wget -qO- \
+         https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
+         tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+    add-apt-repository -y "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+    apt install -y --no-install-recommends r-base r-base-dev
 
-    wget -O /rstudio-server-stretch-1.1.456-amd64.deb \
-      https://download2.rstudio.org/rstudio-server-stretch-1.1.456-amd64.deb
-    gdebi -n /rstudio-server-stretch-1.1.456-amd64.deb
+    wget -O /rstudio-2023.03.0-386-amd64.deb \
+      https://download1.rstudio.org/electron/jammy/amd64/rstudio-2023.03.0-386-amd64.deb
+    apt -y install /rstudio-2023.03.0-386-amd64.deb
+
+    wget -O /rstudio-server-2023.03.0-386-amd64.deb \
+      https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.03.0-386-amd64.deb 
+    apt install -y gdebi-core
+    gdebi -n /rstudio-server-2023.03.0-386-amd64.deb
+
+    # Log to stderr
+    echo "[*]\nlog-level=error\nlogger-type=stderr\n" > /etc/rstudio/logging.conf
 
     # Setup the "general" CRAN repo
     echo 'local({
@@ -24,22 +38,14 @@ From: debian:9
  options(repos = r)
 })' >> /etc/R/Rprofile.site
 
-    # We are setting up a normal user for access
-    # Login: rstudio  Password: rstudio
-    useradd -c "RStudio Account" -u 500 -d /home/rstudio -s /bin/bash rstudio
-    echo "rstudio:rstudio" | /usr/sbin/chpasswd
-
-    # Move systemd service file into place
-    cp /usr/lib/rstudio-server/extras/systemd/rstudio-server.service /lib/systemd/system/
-    systemctl enable rstudio-server
+    # Prepare system to use UTF-8
+    sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && locale-gen && update-locale
 
     # Remove unneeded source packages
-    rm -f /rstudio-1.1.456-amd64.deb
-    rm -f /rstudio-server-stretch-1.1.456-amd64.deb
+    rm -f /rstudio*.deb
 
 %runscript
     /usr/bin/rstudio "$@"
 
 %startscript
-    /usr/lib/rstudio-server/bin/rserver
-
+    /usr/lib/rstudio-server/bin/rserver --server-user=$(whoami)"$@"