enable bioconductor-3.8 (#37)

* enable bioconductor-3.8 * fix ansible-lint * bioconductor refactoring * bioconductor refactoring pass 2 * bioconductor - updated * inverse task order - need to update a package before install an other one * fix old.packages * rename register * Update R-update-package.j2 * re-order package install and update task * remove retries from install and repository task * re-order package install and remove task Co-authored-by: Fanch <[email protected]>
Oefenweb · May 8, 2020 · 40e9c2c · 40e9c2c
1 parent eb94a4c
commit 40e9c2c
Show file tree

Hide file tree

Showing 5 changed files with 60 additions and 12 deletions.
diff --git a/defaults/main.yml b/defaults/main.yml
@@ -14,5 +14,3 @@ r_packages_repos: "{{ r_cran_mirror }}"
 r_packages_lib: /usr/local/lib/R/site-library
 r_packages: []
 r_environment: {}
-
-r_packages_from_github: "{{ r_packages | selectattr('type', 'defined') | selectattr('type', 'equalto', 'github') | map(attribute='name') | list | length > 0 }}"
diff --git a/tasks/packages.yml b/tasks/packages.yml
@@ -31,7 +31,12 @@
   environment: "{{ r_environment }}"
   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, r_packages) }}"
+  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
+        }}"
   when: item.state is undefined or item.state == 'present'
   tags:
     - r-packages-install
@@ -53,11 +58,18 @@
   command: >
     R-update-package
       {{ item.name }}
-      {% if item.lib is defined %}{{ item.lib }}{% endif %}
+      {{ item.type | default(r_packages_type) }}
+      {{ item.lib | default(r_packages_lib) }}
+      {% if item.repos is defined %}{{ item.repos }}{% endif %}
   environment: "{{ r_environment }}"
   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 }}"
+  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
+        }}"
   when: item.state is defined and item.state == 'updated'
   tags:
     - r-packages-update
diff --git a/templates/usr/local/bin/R-install-package.j2 b/templates/usr/local/bin/R-install-package.j2
@@ -34,8 +34,12 @@ if (!(package %in% installed.packages(lib.loc = lib)[, 'Package'])) {
     }, warning = stop);
   } else if (type == 'bioconductor') {
     withCallingHandlers({
-      source('{{ r_bioclite_url }}')
-      biocLite(package, lib = lib, suppressUpdates = TRUE, suppressAutoUpdate = TRUE, ask = FALSE)
+      {% if r_version_35 %}
+        BiocManager::install(package, lib = lib, update = FALSE)
+      {% else %}
+        source('{{ r_bioclite_url }}')
+        biocLite(package, lib = lib, suppressUpdates = TRUE, suppressAutoUpdate = TRUE, ask = FALSE)
+      {% endif %}
       cat("changed\n");
     }, warning = stop);
   } else if (type == 'github') {

diff --git a/templates/usr/local/bin/R-update-package.j2 b/templates/usr/local/bin/R-update-package.j2
@@ -2,17 +2,44 @@
 
 argv = commandArgs(trailingOnly = TRUE);
 if (is.null(argv) | length(argv) < 1) {
-  cat("Usage: R-update-package package [lib] [repos]\n");
+  cat("Usage: R-update-package package [type] [lib] [repos]\n");
   q(status = 1);
 }
 
-package = argv[1];
-lib = ifelse(is.na(argv[2]), '{{ r_packages_lib }}', argv[2]);
-repos = ifelse(is.na(argv[3]), '{{ r_packages_repos.rstrip('/') }}', argv[3]);
+type =  ifelse(is.na(argv[2]), '{{ r_packages_type }}', argv[2]);
+lib = ifelse(is.na(argv[3]), '{{ r_packages_lib }}', argv[3]);
+repos = ifelse(is.na(argv[4]), '{{ r_packages_repos.rstrip('/') }}', argv[4]);
 
-if (package %in% old.packages(lib.loc = lib)[, 'Package']) {
+if (type == 'github') {
+  repo = argv[1];
+  package = unlist(strsplit(repo, "/"))[2];
+} else {
+  package = argv[1];
+}
+
+if (package %in% old.packages(lib.loc = lib, repos = repos)[, 'Package'] & type == 'cran') {
   withCallingHandlers({
     update.packages(package, lib, repos, ask = FALSE);
     cat("changed\n");
   }, warning = stop);
 }
+
+if (type == 'bioconductor') {
+  withCallingHandlers({
+    {% if r_version_35 %}
+      BiocManager::install(package, lib = lib, update = FALSE)
+    {% else %}
+      source('{{ r_bioclite_url }}')
+      biocLite(package, lib = lib, suppressUpdates = TRUE, suppressAutoUpdate = TRUE, ask = FALSE)
+    {% endif %}
+    cat("changed\n");
+  }, warning = stop);
+}
+
+if (type == 'github') {
+  withCallingHandlers({
+    library(remotes)
+    install_github(repo, lib = lib, force = TRUE)
+    cat("changed\n");
+  }, warning = stop);
+}
diff --git a/vars/main.yml b/vars/main.yml
@@ -9,5 +9,12 @@ r_dependencies:
   - r-base
   - "{{ r_install_dev | ternary('r-base-dev', r_dependencies_dummy_package) }}"
 
+r_packages_from_github: "{{ r_packages | selectattr('type', 'defined') | selectattr('type', 'equalto', 'github') | map(attribute='name') | list | length > 0 }}"
+
 r_preset_package_remotes:
   - name: remotes
+
+r_packages_from_bioconductor: "{{ r_packages | selectattr('type', 'defined') | selectattr('type', 'equalto', 'bioconductor') | map(attribute='name') | list | length > 0 }}"
+
+r_preset_package_bioconductor:
+  - name: BiocManager