[DH-337] upgrade R, R studio to latest version on hubs

deployments/biology/image/Dockerfile

@@ -1,4 +1,4 @@
-FROM buildpack-deps:focal-scm
+FROM buildpack-deps:jammy-scm
 
 ENV TZ=America/Los_Angeles
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
@@ -29,22 +29,11 @@ RUN apt-get update -qq --yes > /dev/null && \
     apt-get install --yes -qq \
         libpython2.7 > /dev/null
 
-## libraries required for mothur
-## libreadline6 required
-#RUN apt-get update -qq --yes > /dev/null && \
-#    apt-get install --yes -qq \
-#    libreadline6-dev > /dev/null
-
 ## library required for fast-PCA & https://github.com/DReichLab/EIG
 RUN apt-get update -qq --yes && \
     apt-get install --yes --no-install-recommends -qq \
         libgsl-dev >/dev/null
 
-## library required for running ccb293 package qiime
-#RUN apt-get update -qq --yes > /dev/null && \
-#    apt-get install --yes -qq \
-#    tzdata > /dev/null
-
 # Install these without 'recommended' packages to keep image smaller.
 # Useful utils that folks sort of take for granted
 RUN apt-get update -qq --yes && \
@@ -64,25 +53,48 @@ RUN apt-get update -qq --yes && \
 RUN echo "${LC_ALL} UTF-8" > /etc/locale.gen && \
     locale-gen
 
-RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" > /etc/apt/sources.list.d/cran.list
+# Needed by RStudio
+RUN apt-get update -qq --yes && \
+    apt-get install --yes --no-install-recommends -qq \
+        psmisc \
+        sudo \
+        libapparmor1 \
+        lsb-release \
+        libclang-dev \
+        libpq5 > /dev/null
 
+# Needed by many R libraries
+# Picked up from https://github.com/rocker-org/rocker/blob/9dc3e458d4e92a8f41ccd75687cd7e316e657cc0/r-rspm/focal/Dockerfile
+RUN apt-get update && \
+	apt-get install -y --no-install-recommends \
+                   libgdal-dev \
+                   libgeos3.10.2 \
+                   libproj22 \
+                   libudunits2-0 \
+                   libxml2 > /dev/null
 
-# Install R packages
-# Our pre-built R packages from rspm are built against system libs in focal
-# rstan takes forever to compile from source, and needs libnodejs
-# So we install older (10.x) nodejs from apt rather than newer from conda
-ENV R_VERSION=4.1.2-1.2004.0
+# Install R.
+# These packages must be installed into the base stage since they are in system
+# paths rather than /srv.
+# Pre-built R packages from rspm are built against system libs in jammy.
+ENV R_VERSION=4.4.1-1.2204.0
+ENV LITTLER_VERSION=0.3.19-1.2204.0
 RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" > /etc/apt/sources.list.d/cran.list
+RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" > /etc/apt/sources.list.d/cran.list
+RUN curl --silent --location --fail https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc > /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
 RUN apt-get update -qq --yes > /dev/null && \
     apt-get install --yes -qq \
-    r-base-core=${R_VERSION} \
-    r-base-dev=${R_VERSION} \
-    r-cran-littler=0.3.14-1.2004.0 \
-    libglpk-dev \
-    libzmq5 \
-    nodejs npm > /dev/null
+        r-base-core=${R_VERSION} \
+        r-base-dev=${R_VERSION} \
+        littler=${LITTLER_VERSION} \
+        libglpk-dev \
+        libzmq5 \
+        nodejs npm > /dev/null
+
+ENV RSTUDIO_URL=https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.04.2-764-amd64.deb
+RUN curl --silent --location --fail ${RSTUDIO_URL} > /tmp/rstudio.deb && \
+    apt install --no-install-recommends --yes /tmp/rstudio.deb && \
+    rm /tmp/rstudio.deb
 
 # Install desktop packages
 RUN apt-get update -qq --yes > /dev/null && \
@@ -123,30 +135,6 @@ RUN apt-get update -qq --yes > /dev/null && \
 
 WORKDIR /home/jovyan
 
-# Needed by RStudio
-RUN apt-get update -qq --yes && \
-    apt-get install --yes --no-install-recommends -qq \
-        psmisc \
-        sudo \
-        libapparmor1 \
-        lsb-release \
-        libclang-dev \
-        libpq5 > /dev/null
-
-ENV RSTUDIO_URL https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2021.09.1-372-amd64.deb
-RUN curl --silent --location --fail ${RSTUDIO_URL} > /tmp/rstudio.deb && \
-    dpkg -i /tmp/rstudio.deb && \
-    rm /tmp/rstudio.deb
-
-# Needed by many R libraries
-# Picked up from https://github.com/rocker-org/rocker/blob/9dc3e458d4e92a8f41ccd75687cd7e316e657cc0/r-rspm/focal/Dockerfile
-RUN apt-get update && \
-	apt-get install -y --no-install-recommends \
-                   libgdal26 \
-                   libgeos-3.8.0 \
-                   libproj15 \
-                   libudunits2-0 \
-                   libxml2 > /dev/null
 # R_LIBS_USER is set by default in /etc/R/Renviron, which RStudio loads.
 # We uncomment the default, and set what we wanna - so it picks up
 # the packages we install. Without this, RStudio doesn't see the packages

deployments/biology/image/Rprofile.site

@@ -1,10 +1,10 @@
 # Use RStudio's CRAN mirror to get binary packages
 # 'latest' just means it has all available versions.
 # We can specify version numbers in devtools::install_version
-options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))
+options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/jammy/latest"))
 
 # RStudio's CRAN mirror needs this to figure out which binary package to serve.
 # If not set properly, it will just serve up source packages
 # Quite hilarious, IMO.
 # See https://docs.rstudio.com/rspm/admin/binaries.html
-options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
+options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))

deployments/biology/image/rsession.conf

@@ -1,2 +1,2 @@
 # Use binary packages!
-r-cran-repos=https://packagemanager.rstudio.com/all/__linux__/focal/latest
+r-cran-repos=https://packagemanager.rstudio.com/all/__linux__/jammy/latest

deployments/datahub/images/default/Dockerfile

@@ -50,16 +50,17 @@ RUN install -d -o ${NB_USER} -g ${NB_USER} ${R_LIBS_USER}
 # These packages must be installed into the base stage since they are in system
 # paths rather than /srv.
 # Pre-built R packages from rspm are built against system libs in jammy.
-ENV R_VERSION=4.3.2-1.2204.0
-ENV LITTLER_VERSION=0.3.18-2.2204.0
+#ENV R_VERSION=4.3.2-1.2204.0
+#ENV LITTLER_VERSION=0.3.18-2.2204.0
+ENV R_VERSION=4.4.1-1.2204.0
+ENV LITTLER_VERSION=0.3.19-1.2204.0
 RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
 RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" > /etc/apt/sources.list.d/cran.list
 RUN curl --silent --location --fail https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc > /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
 RUN apt-get update --yes > /dev/null && \
     apt-get install --yes -qq r-base-core=${R_VERSION} r-base-dev=${R_VERSION} littler=${LITTLER_VERSION} > /dev/null
 
-#ENV RSTUDIO_URL https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.06.0-421-amd64.deb
-ENV RSTUDIO_URL https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.12.0-369-amd64.deb
+ENV RSTUDIO_URL=https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.04.2-764-amd64.deb
 RUN curl --silent --location --fail ${RSTUDIO_URL} > /tmp/rstudio.deb && \
     apt install --no-install-recommends --yes /tmp/rstudio.deb && \
     rm /tmp/rstudio.deb

deployments/datahub/images/default/Rprofile.site

@@ -16,8 +16,7 @@ options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/jammy
 # below sets it to be binary. This may improve image build times.
 # If it works, it'd be better to dynamically set the R version as above, and
 # also the RStudio Server version if possible.
-options(HTTPUserAgent = "RStudio Server (2023.12.0.369); R (4.3.2 x86_64-pc-linux-gnu x86_64 linux-gnu)")
-
+options(HTTPUserAgent = "RStudio Server (2024.04.2.764); R (4.4.1 x86_64-pc-linux-gnu x86_64 linux-gnu)")
 
 ## Source extra Rprofile files.
 #

deployments/dev/images/default/Dockerfile

@@ -34,8 +34,8 @@ RUN apt-get -qq update --yes && \
 # These packages must be installed into the base stage since they are in system
 # paths rather than /srv.
 # Pre-built R packages from rspm are built against system libs in jammy.
-ENV R_VERSION=4.3.2-1.2204.0
-ENV LITTLER_VERSION=0.3.18-2.2204.0
+ENV R_VERSION=4.4.1-1.2204.0
+ENV LITTLER_VERSION=0.3.19-1.2204.0
 RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
 RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" > /etc/apt/sources.list.d/cran.list
 RUN curl --silent --location --fail https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc > /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
@@ -45,7 +45,7 @@ RUN apt-get update -qq --yes > /dev/null && \
         r-base-dev=${R_VERSION} \
         littler=${LITTLER_VERSION} > /dev/null
 
-ENV RSTUDIO_URL https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.06.0-421-amd64.deb
+ENV RSTUDIO_URL=https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.04.2-764-amd64.deb
 RUN curl --silent --location --fail ${RSTUDIO_URL} > /tmp/rstudio.deb && \
     apt install --no-install-recommends --yes /tmp/rstudio.deb && \
     rm /tmp/rstudio.deb

deployments/dev/images/default/Rprofile.site

@@ -17,7 +17,7 @@ options(
 options(
   HTTPUserAgent = sprintf(
     "RStudio Server (%s); R (%s)",
-    "2022.7.1.554",
+    "2024.04.2.764",
     paste(getRversion(), R.version$platform, R.version$arch, R.version$os)
   )
 )

deployments/ischool/image/Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/geospatial:4.3.1
+FROM rocker/geospatial:4.4.1
 
 ENV NB_USER rstudio
 ENV NB_UID 1000

deployments/publichealth/image/Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/rocker-org/geospatial:4.3.2
+FROM ghcr.io/rocker-org/geospatial:4.4.1
 
 ENV NB_USER rstudio
 ENV NB_UID 1000

deployments/shiny/image/Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/geospatial:4.3.2
+FROM rocker/geospatial:4.4.1
 
 ENV NB_USER rstudio
 ENV NB_UID 1000
@@ -55,7 +55,7 @@ RUN apt-get update > /dev/null && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-ENV SHINY_SERVER_URL https://download3.rstudio.org/ubuntu-18.04/x86_64/shiny-server-1.5.21.1012-amd64.deb
+ENV SHINY_SERVER_URL https://download3.rstudio.org/ubuntu-18.04/x86_64/shiny-server-1.5.22.1017-amd64.deb
 RUN curl --silent --location --fail ${SHINY_SERVER_URL} > /tmp/shiny-server.deb && \
     apt install --no-install-recommends --yes /tmp/shiny-server.deb && \
     rm /tmp/shiny-server.deb

deployments/stat20/image/Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/geospatial:4.3.2
+FROM rocker/geospatial:4.4.1
 # https://github.com/rocker-org/rocker-versioned2/wiki/geospatial_e06f866673fa
 
 ENV NB_USER rstudio