From 9d36440c951bfb9b7ae591c9b7d29590eda1a628 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@sevenseas.org>
Date: Wed, 3 Feb 2016 16:40:08 +0100
Subject: [PATCH] d4science-ghn-cluster/group_vars/rstudio: New rstudio group.
 Only used to deploy R right now. library/roles/R/tasks/main.yml: Another
 attempt to fix the packages installation workflow.

---
 R/tasks/main.yml                              | 26 +++++++++----------
 .../{Rprofiles.site.j2 => Rprofile.site.j2}   |  0
 2 files changed, 13 insertions(+), 13 deletions(-)
 rename R/templates/{Rprofiles.site.j2 => Rprofile.site.j2} (100%)

diff --git a/R/tasks/main.yml b/R/tasks/main.yml
index 0e754ed..bd74f03 100644
--- a/R/tasks/main.yml
+++ b/R/tasks/main.yml
@@ -34,10 +34,10 @@
 
 - name: Configure the default CRAN mirror
   template: src=Rprofile.site.j2 dest=/etc/R/Rprofile.site owner=root group=root mode=0444
-  when: r_install_cran_repo
+  when: r_install_cran_repo == 'present'
   tags: [ 'r_software', 'r_profile', 'r_pkg' ]
   
-- name: Install some packages needed by R plugins when installed from source, if needed
+- name: Install some packages needed by R packages when installed from source
   apt: pkg={{ item }} state={{ r_packages_state }} update_cache=yes force=yes
   with_items: r_distribution_required_packages
   when: r_needs_additional_distro_pkgs
@@ -48,10 +48,20 @@
   when: r_plugins_from_sources is defined
   tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
 
+- name: Install R packages from the cran sources repo, latest available version
+  command: >
+    Rscript --slave --no-save --no-restore-history -e "if (! ('{{ item }}' %in% installed.packages()[,'Package'])) { install.packages(pkgs='{{ item }}', repos=c('{{ r_cran_mirror_site }}/')); print('Added'); } else { print('Already installed'); }"
+  register: install_plugins_result
+  failed_when: "install_plugins_result.rc != 0 or 'had non-zero exit status' in install_plugins_result.stderr"
+  changed_when: "'Added' in install_plugins_result.stdout"
+  with_items: r_plugins_list_to_install
+  when: r_plugins_install_latest_source
+  tags: [ 'r_software', 'r_pkg', 'r_plugins' ]
+
 - name: Get the R packages sources that need to be installed
   get_url: url={{ item.url }} dest={{ r_source_plugins_dest_dir }}
   with_items: r_plugins_from_sources
-  when: r_plugins_from_sources is defined
+  when: r_plugins_install_specific_source
   tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
   
 - name: Install R packages from the cran sources, specific versions
@@ -75,16 +85,6 @@
   when: r_plugins_install_specific_source
   tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
 
-- name: Install R packages from the cran sources repo, latest version
-  command: >
-    Rscript --slave --no-save --no-restore-history -e "if (! ('{{ item }}' %in% installed.packages()[,'Package'])) { install.packages(pkgs='{{ item }}', repos=c('{{ r_cran_mirror_site }}/')); print('Added'); } else { print('Already installed'); }"
-  register: install_plugins_result
-  failed_when: "install_plugins_result.rc != 0 or 'had non-zero exit status' in install_plugins_result.stderr"
-  changed_when: "'Added' in install_plugins_result.stdout"
-  with_items: r_plugins_list_to_install
-  when: r_plugins_install_latest_source
-  tags: [ 'r_software', 'r_pkg', 'r_plugins' ]
-
 - name: Install R packages from github
   command: >
     Rscript --slave --no-save --no-restore-history -e "if (! ('{{ item.plugin_name }}' %in% installed.packages()[,'Package'])) { require(devtools); require(methods) ; options(repos='{{ r_cran_mirror_site }}/') ; install_github('{{ item.plugin_name }}', '{{ item.github_user }}'); print('Added'); } else { print('Already Installed'); }"
diff --git a/R/templates/Rprofiles.site.j2 b/R/templates/Rprofile.site.j2
similarity index 100%
rename from R/templates/Rprofiles.site.j2
rename to R/templates/Rprofile.site.j2