Allow R4 install (#49)

* enable install of R 4.0 * add a warning about r_version_35 * update readme about r_version and r_version_35 * Allow R4 install * Fixes Co-authored-by: Fanch <[email protected]>
Oefenweb · Jan 19, 2021 · 7b5e07f · 7b5e07f
1 parent 327e0a3
commit 7b5e07f
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Showing 7 changed files with 23 additions and 22 deletions.
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ Set up the latest version of R in Ubuntu systems.
 
 #### Variables
 
-* `r_version_35`: [default: `false`, for `Ubuntu >= 18.04` always `true`]: Whether or not to install R 3.5+
+* `r_version`: [default: `34`, `35` for `Ubuntu >= 18.04`, `40` for `Ubuntu >= 20.04`]: Version to install
 
 * `r_cran_mirror`: [default: `https://cran.rstudio.com/`]: Your favorite [CRAN mirror](https://cran.r-project.org/mirrors.html)
 * `r_bioclite_url`: [default: `https://bioconductor.org/biocLite.R`]: The `biocLite.R` script URL for [Bioconductor](https://bioconductor.org/) installs

diff --git a/Vagrantfile b/Vagrantfile
@@ -5,22 +5,22 @@ role = File.basename(File.expand_path(File.dirname(__FILE__)))
 
 boxes = [
   {
-    :name => "ubuntu-1404",
-    :box => "bento/ubuntu-14.04",
+    :name => "ubuntu-1604",
+    :box => "bento/ubuntu-16.04",
     :ip => '10.0.0.12',
     :cpu => "50",
     :ram => "256"
   },
   {
-    :name => "ubuntu-1604",
-    :box => "bento/ubuntu-16.04",
+    :name => "ubuntu-1804",
+    :box => "bento/ubuntu-18.04",
     :ip => '10.0.0.13',
     :cpu => "50",
-    :ram => "256"
+    :ram => "384"
   },
   {
-    :name => "ubuntu-1804",
-    :box => "bento/ubuntu-18.04",
+    :name => "ubuntu-2004",
+    :box => "bento/ubuntu-20.04",
     :ip => '10.0.0.14',
     :cpu => "50",
     :ram => "384"

diff --git a/defaults/main.yml b/defaults/main.yml
@@ -1,6 +1,6 @@
 # defaults file for r
 ---
-r_version_35: "{{ (ansible_distribution == 'Ubuntu' and ansible_distribution_version is version('18.04', '>=')) }}"
+r_version: "{{ '40' if ansible_distribution_version is version('20.04', '>=') else '35' if ansible_distribution_version is version('18.04', '>=') else '34' }}"
 
 r_cran_mirror: https://cran.rstudio.com/
 r_bioclite_url: https://bioconductor.org/biocLite.R

diff --git a/tasks/packages.yml b/tasks/packages.yml
@@ -32,11 +32,11 @@
   register: _r_install_package
   changed_when: "_r_install_package.stdout_lines[-1] is defined and _r_install_package.stdout_lines[-1] == 'changed'"
   with_items:
-        "{{
-            r_packages_from_github | ternary (r_preset_package_remotes, []) +
-            r_packages_from_bioconductor | ternary ((r_version_35 | ternary (r_preset_package_bioconductor, [])), []) +
-            r_packages
-        }}"
+    "{{
+        r_packages_from_github | ternary (r_preset_package_remotes, []) +
+        r_packages_from_bioconductor | ternary ((r_version is version('35', '>=') | ternary (r_preset_package_bioconductor, [])), []) +
+        r_packages
+    }}"
   when: item.state is undefined or item.state == 'present'
   tags:
     - r-packages-install
@@ -67,11 +67,11 @@
   register: _r_update_package
   changed_when: "_r_update_package.stdout_lines[-1] is defined and _r_update_package.stdout_lines[-1] == 'changed'"
   with_items:
-        "{{
-            r_packages_from_github | ternary (r_preset_package_remotes, []) +
-            r_packages_from_bioconductor | ternary ((r_version_35 | ternary (r_preset_package_bioconductor, [])), []) +
-            r_packages
-        }}"
+    "{{
+        r_packages_from_github | ternary (r_preset_package_remotes, []) +
+        r_packages_from_bioconductor | ternary ((r_version is version('35', '>=') | ternary (r_preset_package_bioconductor, [])), []) +
+        r_packages
+    }}"
   when:
     - item.state is defined
     - item.state == 'updated'

diff --git a/templates/usr/local/bin/R-install-package.j2 b/templates/usr/local/bin/R-install-package.j2
@@ -34,7 +34,7 @@ if (!(package %in% installed.packages(lib.loc = lib)[, 'Package'])) {
     }, warning = stop);
   } else if (type == 'bioconductor') {
     withCallingHandlers({
-      {% if r_version_35 %}
+      {% if r_version is version('35', '>=') %}
         BiocManager::install(package, lib = lib, update = FALSE)
       {% else %}
         source('{{ r_bioclite_url }}')

diff --git a/templates/usr/local/bin/R-update-package.j2 b/templates/usr/local/bin/R-update-package.j2
@@ -26,7 +26,7 @@ if (package %in% old.packages(lib.loc = lib, repos = repos)[, 'Package'] & type
 
 if (type == 'bioconductor') {
   withCallingHandlers({
-    {% if r_version_35 %}
+    {% if r_version is version('35', '>=') %}
       BiocManager::install(package, lib = lib, update = FALSE)
     {% else %}
       source('{{ r_bioclite_url }}')

diff --git a/vars/main.yml b/vars/main.yml
@@ -1,8 +1,9 @@
 # vars file for r
 ---
+r_repository_suffix: "{{ '-cran' + r_version if r_version is version('35', '>=') else '' }}"
 r_repository:
   - type: deb
-    url: "{{ r_cran_mirror }}/bin/linux/{{ ansible_distribution | lower }} {{ ansible_distribution_release }}{{ r_version_35 | ternary('-cran35', '') }}/"
+    url: "{{ r_cran_mirror }}/bin/linux/{{ ansible_distribution | lower }} {{ ansible_distribution_release }}{{ r_repository_suffix }}/"
 
 r_dependencies_pre:
   - apt-transport-https