library/roles/R: task to install R packages from github. Make some steps conditionals.

d4science-ghn-cluster/roles/dataminer_app: First part of the dataminer playbook.

R/defaults/main.yml

@@ -8,19 +8,24 @@
 # The install/remove script has been taken from here: http://adamj.eu/tech/2014/07/19/installing-and-removing-r-packages-with-ansible/
 #
 
-r_install_cran_repo: False
+# Set to present if you want install from CRAN
+r_install_cran_repo: absent
 #r_cran_mirror_site: http://cran.rstudio.com
 r_cran_mirror_site: http://cran.mirror.garr.it/mirrors/CRAN/
+r_base_specific_version: False
 r_base_pkg_version: 2.14.1
 r_packages_state: present
+r_plugins_from_deb: True
+r_plugins_install_latest_source: True
+r_plugins_install_specific_source: True
 
 r_source_plugins_dest_dir: /var/cache/R
 
 r_base_packages_list:
   - r-base
-  - jags
 
 r_plugins_packages_list:
+  - jags
   - r-cran-rjags
   - r-cran-abind
   - r-cran-boot
@@ -41,9 +46,6 @@ r_plugins_packages_list:
   - r-cran-spatial
   - r-cran-survival
 
-# r_plugins_from_sources:
-#   - { name: 'plyr', version: '1.7.1', source: 'plyr_1.7.1.tar.gz', url: 'http://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.7.1.tar.gz' }
-
 r_plugins_list_to_install:
   - R2WinBUGS
   - R2jags
@@ -67,5 +69,13 @@ r_plugins_list_to_install:
   - tools
   - utils
 
+# r_plugins_from_sources:
+#   - { name: 'plyr', version: '1.7.1', source: 'plyr_1.7.1.tar.gz', url: 'http://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.7.1.tar.gz' }
+
+# r_plugins_from_github:
+#   - { plugin_name: 'RFigisGeo', github_user: 'openfigis' }
+#   - { plugin_name: 'rsdmx', github_user: 'opensdmx' }
+
+# Plugins removal not yet implemented
 #r_plugins_list_to_remove:
 

R/tasks/main.yml

@@ -1,48 +1,24 @@
 ---
-- name: Install the cran repository key
+- name: Manage the cran repository key
-  apt_key: id=E084DAB9 keyserver=keyserver.ubuntu.com state=present
+  apt_key: id=E084DAB9 keyserver=keyserver.ubuntu.com state={{ r_install_cran_repo }}
-  register: update_apt_cache
+  tags: [ 'r_software', 'r_repo' ]
-  when: r_install_cran_repo
-  tags:
-    - r_software
-    - r_repo
 
-- name: Install the cran repository definition
+- name: Manage the cran repository definition
-  apt_repository: repo='deb http://cran.rstudio.com/bin/linux/ubuntu {{ ansible_distribution_release }}/' state=present
+  apt_repository: repo='deb http://cran.rstudio.com/bin/linux/ubuntu {{ ansible_distribution_release }}/' state={{ r_install_cran_repo }} update_cache=yes
-  register: update_apt_cache
+  tags: [ 'r_software', 'r_repo' ]
-  when: r_install_cran_repo
-  tags:
-    - r_software
-    - r_repo
 
-- name: Install the cran repository definition
+#
-  apt_repository: repo='deb {{ r_cran_mirror_site }}/bin/linux/ubuntu {{ ansible_distribution_release }}/' state=absent
+# This does not work. It resolves dependecies badly and/or installs the right version only for one of the packages
-  register: update_apt_cache
+- name: Install a specific version of the R base package
-  when: not r_install_cran_repo
-  tags:
-    - r_software
-    - r_repo
-
-- name: Update the apt cache if needed
-  apt: update_cache=yes
-  when: ( update_apt_cache | changed )
-  tags:
-    - r_software
-    - r_repo
-
-- name: Install the R base packages
   apt: pkg={{ item }} state={{ r_packages_state }}
   with_items: r_base_packages_list
-  tags:
+  tags: [ 'r_software', 'r_pkg' ]
-    - r_software
-    - r_pkg
 
-- name: Install the R plugins from the ubuntu repo
+- name: Install the R additional modules from the deb repo
   apt: pkg={{ item }} state={{ r_packages_state }}
   with_items: r_plugins_packages_list
-  tags:
+  when: r_plugins_from_deb
-    - r_software
+  tags: [ 'r_software', 'r_pkg' ]
-    - r_pkg
 
 - name: Ensure that the R plugin sources directory exists
   file: dest={{ r_source_plugins_dest_dir }} state=directory owner=root group=root
@@ -55,23 +31,33 @@
   when: r_plugins_from_sources is defined
   tags: [ 'r_software', 'r_pkg', 'r_plugins' ]
   
-- name: Install R plugins from the cran sources
+- name: Install R plugins from the cran sources, specific versions
   command: >
     Rscript --slave --no-save --no-restore-history -e "if (! ('{{ item.name }}' %in% installed.packages()[,'Package'])) { install.packages('{{ r_source_plugins_dest_dir }}/{{ item.source }}', repos = NULL, type='source'); print('Added'); } else { print('Already Installed'); }"
   register: install_s_plugins_result
   failed_when: "install_s_plugins_result.rc != 0 or 'had non-zero exit status' in install_s_plugins_result.stderr"
   changed_when: "'Added' in install_s_plugins_result.stdout"
   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' ]
 
-- name: Install R plugins from the cran binaries repo
+- name: Install R plugins 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 plugins 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'); }"
+  register: install_s_plugins_result
+  failed_when: "install_s_plugins_result.rc != 0 or 'had non-zero exit status' in install_s_plugins_result.stderr"
+  changed_when: "'Added' in install_s_plugins_result.stdout"
+  with_items: r_plugins_from_github
+  when: r_plugins_from_github is defined
+  tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github' ]
 

ubuntu-deb-general/files/backports-squeeze

@@ -0,0 +1,3 @@
+Package: *
+Pin: release a=squeeze-backports
+Pin-Priority: 600

ubuntu-deb-general/tasks/packages.yml

@@ -1,67 +1,46 @@
 ---
-- name: install iotop backport PPA
-  copy: src=files/hardy-iotop-ppa dest=/etc/apt/sources.list.d/iotop-ppa.list
-  when: is_hardy
-  notify: apt update
-  tags:
-    - packages
-
-- name: GPG key for iotop backport PPA
-  shell: apt-key list | grep -q 4B1E287796DD5C9A || gpg --keyserver keyserver.ubuntu.com --recv 4B1E287796DD5C9A; gpg --export --armor 4B1E287796DD5C9A | sudo apt-key add -
-  when: is_hardy
-  tags:
-    - packages
-
 - name: Install the basic packages
   apt: pkg=python-software-properties state=installed
-  when: has_apt
+  tags: packages
-  tags:
-    - packages
 
 - name: Install software-properties-common if needed
   apt: pkg=software-properties-common state=installed
   when: is_quantal
-  tags:
+  tags: packages
-    - packages
 
-- name: Install the backports repository on debian 6
+- name: Default the backports repository on debian 6
-  apt_repository: repo='deb http://http.debian.net/debian-backports squeeze-backports main' state=present
+  copy: src=backports-squeeze dest=/etc/apt/preferences.d/backports owner=root group=root mode=644
-  register: update_apt_cache
   when: is_debian6
   tags: squeeze-backports
 
-- name: Install the backports repository on debian 7
+- name: Install the backports repository on debian 6
-  apt_repository: repo='deb http://http.debian.net/debian wheezy-backports main' state=present
+  apt_repository: repo='deb http://http.debian.net/debian-backports squeeze-backports main' state=present update_cache=yes
-  register: update_apt_cache
+  when: is_debian6
+  tags: squeeze-backports
+
+- name: Default the backports repository on debian 7
+  copy: src=backports-wheezy dest=/etc/apt/preferences.d/backports owner=root group=root mode=644
   when: is_debian7
   tags: wheezy-backports
 
-- name: Default the backports repository on debian 7
+- name: Install the backports repository on debian 7
-  copy: src=backports dest=/etc/apt/preferences.d owner=root group=root mode=644
+  apt_repository: repo='deb http://http.debian.net/debian wheezy-backports main' state=present update_cache=yes
-  register: update_apt_cache
   when: is_debian7
-  tags: Default-wheezy-backports
+  tags: wheezy-backports
 
 - name: Install the backports repository on debian 8
-  apt_repository: repo='deb http://http.debian.net/debian jessie-backports main' state=present
+  apt_repository: repo='deb http://http.debian.net/debian jessie-backports main' state=present update_cache=yes
-  register: update_apt_cache
   when: is_debian8
   tags: jessie-backports
 
 # Debian 7 “Wheezy” from February 2016 to May 2018
 # Debian 8 “Jessie“ from May 2018 to April/May 2020
 - name: Install the squeeze-lts repository on debian 6
-  apt_repository: repo='deb http://http.debian.net/debian squeeze-lts main contrib non-free' state=present
+  apt_repository: repo='deb http://http.debian.net/debian squeeze-lts main contrib non-free' state=present update_cache=yes
   register: update_apt_cache
   when: is_debian6
   tags: squeeze-lts
 
-# - name: Install the wheezy-lts repository on debian 7
-#   apt_repository: repo='deb http://http.debian.net/debian wheezy-lts main contrib non-free' state=present
-#   register: update_apt_cache
-#   when: is_debian7
-#   tags: wheeze-lts
-
 - name: apt key for the internal ppa repository
   apt_key: url=http://ppa.research-infrastructures.eu/system/keys/system-archive.asc state=present
   when: is_ubuntu