Update base Fedora images

.github/workflows/deploy.yaml

@@ -21,21 +21,23 @@ on:
           - rocker
           - rhub
       distribution:
-        description: Rocker/RHub Distro Name. Eg. rstudio or fedora-gcc-devel
+        description: Rocker/RHub Distro Name.
         required: true
         type: choice
         default: rstudio
         options:
           - rstudio
           - rstudio-local
-          - debian-clang-devel
-          - debian-gcc-devel
-          - fedora-clang-devel
-          - fedora-gcc-devel
-          - debian-gcc-patched
-          - debian-gcc-release
+          - gcc13
+          - gcc14
+          - atlas
+          - valgrind
+          - intel
+          - nosuggests
+          - mkl
       r_version:
-        description: R Version
+        description: |
+          R version (also used as the tag to pull the origin image).
         required: true
         type: choice
         default: "4.4.0"
@@ -54,7 +56,9 @@ on:
           - "4.4.0"
           - "latest"
       latest_r_version:
-        description: "R Version to be aliased as the 'latest' tag"
+        description: |
+          R Version to be aliased as the 'latest' tag".
+          (Only relevant for rocker images).
         required: false
         type: string
         default: "4.4.0"
@@ -73,7 +77,9 @@ on:
           - "3.19"
           - "devel"
       latest_bioc_version:
-        description: "BioC Version to be aliased as the 'latest' tag"
+        description: |
+          BioC Version to be aliased as the 'latest' tag".
+          (Only relevant for rocker images).
         required: false
         type: string
         default: "3.19"
@@ -205,7 +211,8 @@ jobs:
         run: |
           # Set Image name
           image_name="${{ needs.normalize-inputs.outputs.distribution }}_${{ needs.normalize-inputs.outputs.r_version }}_bioc_${{ needs.normalize-inputs.outputs.bioc_version }}"
-          if [[ "${{ needs.normalize-inputs.outputs.distribution }}" =~ ^debian.*|^fedora.* ]]
+          # For Fedora-based rhub images.
+          if [[ "${{ needs.normalize-inputs.outputs.distribution }}" =~ ^gcc.*|^atlas$|^valgrind$|^intel$|^nosuggests$|^mkl$ ]]
           then {
             image_name="${{ needs.normalize-inputs.outputs.distribution }}"
           }

.github/workflows/scheduled.yaml

@@ -46,27 +46,31 @@ jobs:
             origin: rocker
           - distro_tag: 'latest'
             bioc: 'devel'
-            distro: debian-clang-devel
+            distro: gcc13
             origin: rhub
           - distro_tag: 'latest'
             bioc: 'devel'
-            distro: debian-gcc-devel
+            distro: gcc14
             origin: rhub
           - distro_tag: 'latest'
             bioc: 'devel'
-            distro: fedora-clang-devel
+            distro: atlas
             origin: rhub
           - distro_tag: 'latest'
             bioc: 'devel'
-            distro: fedora-gcc-devel
+            distro: valgrind
             origin: rhub
           - distro_tag: 'latest'
-            bioc: '3.19'
-            distro: debian-gcc-patched
+            bioc: 'devel'
+            distro: intel
             origin: rhub
           - distro_tag: 'latest'
-            bioc: '3.19'
-            distro: debian-gcc-release
+            bioc: 'devel'
+            distro: nosuggests
+            origin: rhub
+          - distro_tag: 'latest'
+            bioc: 'devel'
+            distro: mkl
             origin: rhub
 
     # Trigger steps

Dockerfile

@@ -32,6 +32,13 @@ COPY --chmod=0755 [\
     "./"\
 ]
 
+# In order to have predictable results from TinyTex installer, set a reliable CTAN mirror.
+# This variable is used by:
+# https://yihui.org/gh/tinytex/tools/install-base.sh
+# which is in turn used by:
+# https://raw.githubusercontent.com/yihui/tinytex/master/tools/install-unx.sh.
+ENV CTAN_REPO https://mirrors.mit.edu/CTAN/systems/texlive/tlnet
+
 # Install sysdeps
 RUN ./install_sysdeps.sh ${DISTRIBUTION}
 

scripts/install_bioc_pkgs.R

@@ -30,12 +30,13 @@ shared_pkgs <- c(
 bioc_pkgs <- list(
   rstudio = shared_pkgs,
   `rstudio-local` = shared_pkgs,
-  `debian-clang-devel` = shared_pkgs,
-  `debian-gcc-devel` = shared_pkgs,
-  `fedora-clang-devel` = shared_pkgs,
-  `fedora-gcc-devel` = shared_pkgs,
-  `debian-gcc-patched` = shared_pkgs,
-  `debian-gcc-release` = shared_pkgs
+  `gcc13` = shared_pkgs,
+  `gcc14` = shared_pkgs,
+  `atlas` = shared_pkgs,
+  `valgrind` = shared_pkgs,
+  `intel` = shared_pkgs,
+  `nosuggests` = shared_pkgs,
+  `mkl` = shared_pkgs
 )
 
 # Get diff of installed and uninstalled packages for
@@ -44,6 +45,14 @@ new_pkgs <- bioc_pkgs[[distribution]][
   !(bioc_pkgs[[distribution]] %in% installed.packages()[, "Package"])
 ]
 
+# cmdstanr is available on r-universe.dev.
+install.packages(
+  "cmdstanr",
+  repos='https://stan-dev.r-universe.dev'
+)
+
+cmdstanr::install_cmdstan()
+
 # Install only uninstalled packages
 if (length(new_pkgs)) {
   BiocManager::install(new_pkgs,

scripts/install_cran_pkgs.R

@@ -239,12 +239,13 @@ cran_pkgs <- list(
     pharmaverse_pkgs,
     local_dev_packages
   ),
-  `debian-clang-devel` = shared_pkgs,
-  `debian-gcc-devel` = shared_pkgs,
-  `fedora-clang-devel` = shared_pkgs[!shared_pkgs %in% c("rjags")],
-  `fedora-gcc-devel` = shared_pkgs[!shared_pkgs %in% c("rjags")],
-  `debian-gcc-patched` = shared_pkgs,
-  `debian-gcc-release` = shared_pkgs
+  `gcc13` = shared_pkgs[!shared_pkgs %in% c("rjags")],
+  `gcc14` = shared_pkgs[!shared_pkgs %in% c("rjags")],
+  `atlas` = shared_pkgs[!shared_pkgs %in% c("rjags")],
+  `valgrind` = shared_pkgs[!shared_pkgs %in% c("rjags")],
+  `intel` = shared_pkgs[!shared_pkgs %in% c("rjags")],
+  `nosuggests` = shared_pkgs[!shared_pkgs %in% c("rjags")],
+  `mkl` = shared_pkgs[!shared_pkgs %in% c("rjags")]
 )
 
 # Re-install packages with newer versions
@@ -270,7 +271,7 @@ if (length(new_pkgs_from_src)) {
 }
 
 # Install rjags with special params for fedora distros
-if (startsWith(distribution, "fedora")) {
+if (startsWith(distribution, "gcc") || distribution == "atlas" || distribution == "valgrind" || distribution == "intel" || distribution == "nosuggests" || distribution == "mkl") {
   install.packages(
     "rjags",
     type = "source",

scripts/install_gh_pkgs.R

@@ -17,12 +17,13 @@ shared_pkgs <- c(
 gh_pkgs <- list(
   rstudio = shared_pkgs,
   `rstudio-local` = shared_pkgs,
-  `debian-clang-devel` = shared_pkgs,
-  `debian-gcc-devel` = shared_pkgs,
-  `fedora-clang-devel` = shared_pkgs,
-  `fedora-gcc-devel` = shared_pkgs,
-  `debian-gcc-patched` = shared_pkgs,
-  `debian-gcc-release` = shared_pkgs
+  `gcc13` = shared_pkgs,
+  `gcc14` = shared_pkgs,
+  `atlas` = shared_pkgs,
+  `valgrind` = shared_pkgs,
+  `intel` = shared_pkgs,
+  `nosuggests` = shared_pkgs,
+  `mkl` = shared_pkgs
 )
 
 # Get diff of installed and uninstalled packages for

scripts/install_other_pkgs.R

@@ -32,12 +32,13 @@ other_pkgs <- list(
     pharmaverse_packages,
     stat_pkgs
   ),
-  `debian-clang-devel` = c(stat_pkgs),
-  `debian-gcc-devel` = c(stat_pkgs),
-  `fedora-clang-devel` = c(stat_pkgs),
-  `fedora-gcc-devel` = c(stat_pkgs),
-  `debian-gcc-patched` = c(stat_pkgs),
-  `debian-gcc-release` = c(stat_pkgs)
+  `gcc13` = c(stat_pkgs),
+  `gcc14` = c(stat_pkgs),
+  `atlas` = c(stat_pkgs),
+  `valgrind` = c(stat_pkgs),
+  `intel` = c(stat_pkgs),
+  `nosuggests` = c(stat_pkgs),
+  `mkl` = c(stat_pkgs)
 )
 
 # Get diff of installed and uninstalled packages for

scripts/install_pip_pkgs.py

@@ -31,12 +31,13 @@ def install(packages=[]):
     + [
         "pre-commit",
     ],
-    "debian-clang-devel": [],
-    "debian-gcc-devel": [],
-    "fedora-clang-devel": [],
-    "fedora-gcc-devel": [],
-    "debian-gcc-patched": [],
-    "debian-gcc-release": [],
+    "gcc13": [],
+    "gcc14": [],
+    "atlas": [],
+    "valgrind": [],
+    "intel": [],
+    "nosuggests": [],
+    "mkl": [],
 }
 
 # Install packages

scripts/install_sysdeps.sh

@@ -112,34 +112,17 @@ less \
 nano \
 "
 
-# Deps specific on the debian-clang-devel image
-pkgs_to_install_debian["debian-clang-devel"]="${shared_deps_debian} \
-jags \
-"
-
-# Deps specific on the debian-gcc-devel image
-pkgs_to_install_debian["debian-gcc-devel"]="${shared_deps_debian} \
-jags \
-"
-
-# Deps specific on the debian-gcc-patched image
-pkgs_to_install_debian["debian-gcc-patched"]="${shared_deps_debian} \
-jags \
-"
-
-# Deps specific on the debian-gcc-release image
-pkgs_to_install_debian["debian-gcc-release"]="${shared_deps_debian} \
-jags \
-"
-
-# Deps specific on the fedora-gcc-devel image
-pkgs_to_install_fedora["fedora-gcc-devel"]="${shared_deps_fedora}"
-
-# Deps specific on the fedora-clang-devel image
-pkgs_to_install_fedora["fedora-clang-devel"]="${shared_deps_fedora}"
+# Deps specific to the Fedora-based rhub image.
+pkgs_to_install_fedora["gcc13"]="${shared_deps_fedora}"
+pkgs_to_install_fedora["gcc14"]="${shared_deps_fedora}"
+pkgs_to_install_fedora["atlas"]="${shared_deps_fedora}"
+pkgs_to_install_fedora["valgrind"]="${shared_deps_fedora}"
+pkgs_to_install_fedora["intel"]="${shared_deps_fedora}"
+pkgs_to_install_fedora["nosuggests"]="${shared_deps_fedora}"
+pkgs_to_install_fedora["mkl"]="${shared_deps_fedora}"
 
 # Perform installations for debian distros
-if [[ "$distribution" =~ ^rstudio.*|^debian.* ]]
+if [[ "$distribution" =~ ^rstudio.* ]]
 then {
     # Set env vars
     export DEBIAN_FRONTEND=noninteractive
@@ -190,7 +173,7 @@ then {
 }
 fi
 
-if [[ "$distribution" =~ ^fedora.* ]]
+if [[ "$distribution" =~ ^gcc.*|^atlas$|^valgrind$|^intel$|^nosuggests$|^mkl$ ]]
 then {
     # Update
     dnf update -y