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ansible-role-R
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First commit.

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Andrea Dell'Amico 2021-02-25 14:09:55 +01:00
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151
README.md
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@ -1,31 +1,146 @@
Role Name
=========
A brief description of the role goes here.
Requirements
------------
Any pre-requisites that may not be covered by Ansible itself or the role should be mentioned here. For instance, if the role uses the EC2 module, it may be a good idea to mention in this section that the boto package is required.
A role that installs the R environment, <https://cran.r-project.org>
Role Variables
--------------
A description of the settable variables for this role should go here, including any variables that are in defaults/main.yml, vars/main.yml, and any variables that can/should be set via parameters to the role. Any variables that are read from other roles and/or the global scope (ie. hostvars, group vars, etc.) should be mentioned here as well.
The most important variables are listed below:
``` yaml
# Set to True if you want install from the CRAN deb repository
r_install_cran_repo: False
#r_cran_mirror_site: http://cran.rstudio.com
r_cran_set_default_mirror: True
r_cran_mirror_site: https://cran.mirror.garr.it/mirrors/CRAN/
r_base_specific_version: False
r_base_pkg_version: 3.4.4
r_packages_main_state: present
r_packages_state: '{{ r_packages_main_state }}'
r_sitelib_path: '/usr/local/lib/R/site-library'
r_plugins_from_deb: True
r_packages_cleanup: False
#
r_packages_updater: False
r_package_updater_via_subversion: True
r_package_updater_subversion_repo: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/
r_packages_svn_base_dir: /srv/r_updater
r_packages_svn_files_prefix: ''
r_packages_updater_also_upgrades_installed_packages: False
# They need to be flat text files
# 1 package per line
#r_debian_packages_list_url
# package[:cran mirror]
# The CRAN mirror URL is optional
#r_cran_packages_list_url
# The CRAN mirror URL is optional
#r_cran_packages_list_url
# user/package_name
#r_github_packages_list_url
r_source_plugins_dest_dir: /var/cache/R
r_distribution_required_packages: []
# - gdal-bin
# - dans-gdal-scripts
# - libgdal1-dev
# - libgeos-dev
# - libspatialite-dev
# - proj
# - proj-bin
# - proj-data
# - libproj-dev
r_base_packages_list:
- r-base
# Some packages must be put on hold
r_base_packages_hold_list: []
r_plugins_packages_list:
- jags
- r-cran-rjags
- r-cran-abind
- r-cran-boot
- r-cran-class
- r-cran-cluster
- r-cran-coda
- r-cran-codetools
- r-cran-foreign
- r-cran-lattice
- r-cran-maptools
- r-cran-mass
- r-cran-matrix
- r-cran-mgcv
- r-cran-nlme
- r-cran-nnet
- r-cran-rpart
- r-cran-sp
- r-cran-spatial
- r-cran-survival
r_apt_additional_repos:
- 'ppa:opencpu/jq'
# RHEL/CentOS:
# http://springdale.princeton.edu/data/springdale/7/x86_64/os/Computational/
#
r_sitelib_el_path: '/usr/local/lib/R/library'
r_el_dev_pkgs: True
r_base_packages_el:
- R
- R-core
- libRmath
r_base_packages_dev_el:
- R-core-devel
- libRmath-devel
r_base_packages_java_el:
- R-java
r_base_packages_java_dev_el:
- R-java-devel
r_plugins_list_to_install: []
# - { name: 'R2WinBUGS', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'R2jags', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'bayesmix', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'coda', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'rjags', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'runjags', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'base', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'compiler', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'datasets', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'grDevices', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'graphics', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'grid', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'methods', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'parallel', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'reshape', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'splines', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'stats', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'stats4', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'tcltk', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'tools', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'utils', repo: '{{ r_cran_mirror_site }}' }
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' }
#
r_plugins_list_to_remove: []
```
Dependencies
------------
A list of other roles hosted on Galaxy should go here, plus any details in regards to parameters that may need to be set for other roles, or variables that are used from other roles.
Example Playbook
----------------
Including an example of how to use your role (for instance, with variables passed in as parameters) is always nice for users too:
- hosts: servers
roles:
- { role: username.rolename, x: 42 }
None
License
-------
@ -35,4 +150,4 @@ EUPL-1.2
Author Information
------------------
An optional section for the role authors to include contact information, or a website (HTML is not allowed).
Andrea Dell'Amico, <andrea.dellamico@isti.cnr.it>

138
defaults/main.yml
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---
# defaults file for ansible-role-template
#
# There's an untrusted Ubuntu PPA repository with gobs of packages and dependencies: https://launchpad.net/~marutter/+archive/ubuntu/c2d4u
#
# To list the installed R packages
# Run R, then execute
# packinfo <- installed.packages (fields = c ("Package", "Version"))
# packinfo[,c("Package", "Version")]
#
# The install/remove script has been taken from here: http://adamj.eu/tech/2014/07/19/installing-and-removing-r-packages-with-ansible/
#
# Set to True if you want install from the CRAN deb repository
r_install_cran_repo: False
#r_cran_mirror_site: http://cran.rstudio.com
r_cran_set_default_mirror: True
r_cran_mirror_site: https://cran.mirror.garr.it/mirrors/CRAN/
r_base_specific_version: False
r_base_pkg_version: 3.4.4
r_packages_main_state: present
r_packages_state: '{{ r_packages_main_state }}'
r_sitelib_path: '/usr/local/lib/R/site-library'
r_plugins_from_deb: True
r_packages_cleanup: False
#
r_packages_updater: False
r_package_updater_via_subversion: True
r_package_updater_subversion_repo: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/
r_packages_svn_base_dir: /srv/r_updater
r_packages_svn_files_prefix: ''
r_packages_updater_also_upgrades_installed_packages: False
# They need to be flat text files
# 1 package per line
#r_debian_packages_list_url
#r_el_packages_list_url
# package[:cran mirror]
# The CRAN mirror URL is optional
#r_cran_packages_list_url
# The CRAN mirror URL is optional
#r_cran_packages_list_url
# user/package_name
#r_github_packages_list_url
r_source_plugins_dest_dir: /var/cache/R
r_distribution_required_packages: []
# - gdal-bin
# - dans-gdal-scripts
# - libgdal1-dev
# - libgeos-dev
# - libspatialite-dev
# - proj
# - proj-bin
# - proj-data
# - libproj-dev
r_base_packages_list:
- r-base
# Some packages must be put on hold
r_base_packages_hold_list: []
r_plugins_packages_list:
- jags
- r-cran-rjags
- r-cran-abind
- r-cran-boot
- r-cran-class
- r-cran-cluster
- r-cran-coda
- r-cran-codetools
- r-cran-foreign
- r-cran-lattice
- r-cran-maptools
- r-cran-mass
- r-cran-matrix
- r-cran-mgcv
- r-cran-nlme
- r-cran-nnet
- r-cran-rpart
- r-cran-sp
- r-cran-spatial
- r-cran-survival
r_apt_additional_repos:
- 'ppa:opencpu/jq'
# RHEL/CentOS:
# http://springdale.princeton.edu/data/springdale/7/x86_64/os/Computational/
#
r_sitelib_el_path: '/usr/local/lib/R/library'
r_el_dev_pkgs: True
r_base_packages_el:
- R
- R-core
- libRmath
r_base_packages_dev_el:
- R-core-devel
- libRmath-devel
r_base_packages_java_el:
- R-java
r_base_packages_java_dev_el:
- R-java-devel
r_plugins_list_to_install: []
# - { name: 'R2WinBUGS', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'R2jags', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'bayesmix', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'coda', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'rjags', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'runjags', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'base', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'compiler', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'datasets', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'grDevices', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'graphics', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'grid', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'methods', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'parallel', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'reshape', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'splines', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'stats', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'stats4', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'tcltk', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'tools', repo: '{{ r_cran_mirror_site }}' }
# - { name: 'utils', repo: '{{ r_cran_mirror_site }}' }
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' }
#
r_plugins_list_to_remove: []

15
files/r_packages_cleanup.sh Normal file
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#!/bin/bash
# Put the base packages to unhold
for package in r-base r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended ; do apt-mark unhold $package; done
# Remove the old r packages
apt-get purge r-base-* r-cran-* -y --force-yes
apt-get autoremove -y
apt-get update
# Remove the CRAN packages
rm -fr /usr/lib/R/site-library /usr/local/lib/R/site-library
rm -fr /var/cache/R/*
exit 0

47
meta/main.yml
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galaxy_info:
author: your name
description: your description
company: your company (optional)
author: Andrea Dell'Amico
description: Systems Architect
company: ISTI-CNR
# If the issue tracker for your role is not on github, uncomment the
# next line and provide a value
issue_tracker_url: https://support.d4science.org/projects/automatic-provisioning/issues
issue_tracker_url: https://redmine-s2i2s.isti.cnr.it/projects/provisioning
license: EUPL-1.2
license: EUPL 1.2+
min_ansible_version: 2.8
# If this a Container Enabled role, provide the minimum Ansible Container version.
# min_ansible_container_version:
# Optionally specify the branch Galaxy will use when accessing the GitHub
# repo for this role. During role install, if no tags are available,
# Galaxy will use this branch. During import Galaxy will access files on
# this branch. If Travis integration is configured, only notifications for this
# branch will be accepted. Otherwise, in all cases, the repo's default branch
# (usually master) will be used.
#github_branch:
#
# Provide a list of supported platforms, and for each platform a list of versions.
# If you don't wish to enumerate all versions for a particular platform, use 'all'.
# To view available platforms and versions (or releases), visit:
# https://galaxy.ansible.com/api/v1/platforms/
#
platforms:
- name: Ubuntu
versions:
- bionic
- name: Ubuntu
versions:
- bionic
- name: EL
versions:
- 7
galaxy_tags: []
# List tags for your role here, one per line. A tag is a keyword that describes
# and categorizes the role. Users find roles by searching for tags. Be sure to
# remove the '[]' above, if you add tags to this list.
#
# NOTE: A tag is limited to a single word comprised of alphanumeric characters.
# Maximum 20 tags per role.
galaxy_tags:
- R
- CRAN
dependencies: []
# List your role dependencies here, one per line. Be sure to remove the '[]' above,
# if you add dependencies to this list.

11
tasks/main.yml
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---
# tasks file for ansible-role-template
- import_tasks: r-packages_cleanup.yml
when:
- r_packages_cleanup
- ansible_distribution_file_variety == "Debian"
- import_tasks: r-installation-deb.yml
when: ansible_distribution_file_variety == "Debian"
- import_tasks: r-installation-el.yml
when: ansible_distribution_file_variety == "RedHat"
- import_tasks: r-packages-install.yml
- import_tasks: r-packages-updater.yml

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tasks/r-installation-deb.yml Normal file
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---
- block:
- name: Add the cran repository key
apt_key: id=E084DAB9 keyserver=keyserver.ubuntu.com state=present
tags: [ 'r_software', 'r_repo', 'r_repo_key' ]
- name: Add the CRAN repository
apt_repository: repo='deb http://cran.rstudio.com/bin/linux/ubuntu {{ ansible_distribution_release }}/' state=present update_cache=yes
when: r_install_cran_repo
tags: [ 'r_software', 'r_repo' ]
- block:
- name: Remove the CRAN repository
apt_repository: repo='deb http://cran.rstudio.com/bin/linux/ubuntu {{ ansible_distribution_release }}/' state=absent update_cache=yes
when: not r_install_cran_repo
tags: [ 'r_software', 'r_repo' ]
- block:
- name: Remove the hold state from the debian R packages
shell: apt-mark unhold {{ item }}
with_items: '{{ r_base_packages_hold_list | default([]) }}'
when: r_base_packages_hold_list is defined
ignore_errors: True
tags: [ 'r_software', 'r_pkg', 'r_pkg_hold' ]
- name: Install the R base packages.
apt: pkg={{ r_base_packages_list }} state={{ r_packages_main_state }} force=yes update_cache=yes cache_valid_time=3600
- name: When we install specific R deb packages, put them on hold
shell: apt-mark hold {{ item }}
with_items: '{{ r_base_packages_hold_list| default([]) }}'
when: r_base_specific_version
ignore_errors: True
tags: [ 'r_software', 'r_pkg', 'r_pkg_hold' ]
- name: Install the R additional modules from the deb repo
apt: pkg={{ r_plugins_packages_list | default([]) }} state={{ r_packages_state }} force=yes
when: r_plugins_from_deb
- name: Install some additional repositories. They provide dependencies for some R packages
apt_repository: repo={{ item }} state=present update_cache=yes
with_items: '{{ r_apt_additional_repos }}'
when: ansible_distribution_version is version_compare('18.04', '<')
tags: [ 'r_software', 'r_apt_repo', 'r_deps' ]
- name: Install some packages needed by R packages when installed from source
apt: pkg={{ r_distribution_required_packages | default([]) }} state={{ r_packages_state }} update_cache=yes force=yes cache_valid_time=3600
tags: [ 'r_software', 'r_pkg', 'r_deps' ]
tags: [ 'r_software', 'r_pkg' ]

24
tasks/r-installation-el.yml Normal file
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---
- block:
- name: Install the R base packages.
yum: pkg={{ r_base_packages_el }} state={{ r_packages_main_state }}
- name: Install the R base development packages.
yum: pkg={{ r_base_packages_dev_el }} state={{ r_packages_main_state }}
when: r_el_dev_pkgs
- name: Install the R java base packages.
yum: pkg={{ r_base_packages_java_el }} state={{ r_packages_main_state }}
when: jdk_java_home is defined
- name: Install the R java base development packages.
yum: pkg={{ r_base_packages_java_dev_el }} state={{ r_packages_main_state }}
when:
- jdk_java_home is defined
- r_el_dev_pkgs
- name: Install some packages needed by R packages when installed from source
yum: pkg={{ r_distribution_required_el_packages }} state={{ r_packages_state }}
tags: [ 'r_software', 'r_pkg', 'r_deps' ]
tags: [ 'r_software', 'r_pkg' ]

77
tasks/r-packages-install.yml Normal file
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---
- block:
- 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 == 'present'
tags: [ 'r_software', 'r_profile', 'r_pkg' ]
- name: Configure the JDK environment
shell: export JAVA_HOME={{ jdk_java_home }} ; export J2SDKDIR={{ jdk_java_home }} ; export J2REDIR={{ jdk_java_home }}/jre ; R CMD javareconf ; touch /etc/R/.java{{ jdk_default }}.env_conf
args:
creates: '/etc/R/.java{{ jdk_default }}.env_conf'
when:
- jdk_java_home is defined
- jdk_default is defined
tags: [ 'r_software', 'r_profile', 'r_pkg', 'r_java' ]
- name: Ensure that the R packages sources directory exists
file: dest={{ r_source_plugins_dest_dir }} state=directory owner=root group=root
when: r_plugins_from_sources is defined
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
- block:
- name: Install R packages from the cran sources repo or from an alternative repository, latest available version. First try
command: >
Rscript --slave --no-save --no-restore-history -e "if (! ('{{ item.name }}' %in% installed.packages()[,'Package'])) { install.packages(pkgs='{{ item.name }}', repos=c('{{ item.repo | default ('https://cloud.r-project.org') }}/')); 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 | default([]) }}'
ignore_errors: True
- 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 | default([]) }}'
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
- name: Install R packages from the cran sources, specific versions. First round
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 if (packageVersion('{{ item.name }}') != '{{ item.version }}') { 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 | default([]) }}'
ignore_errors: True
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
- 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.github_user }}/{{ item.plugin_name }}'); print('Added'); } else { print('Already Installed'); }"
register: install_github_plugins_result
failed_when: "install_github_plugins_result.rc != 0 or 'had non-zero exit status' in install_github_plugins_result.stderr"
changed_when: "'Added' in install_github_plugins_result.stdout"
with_items: '{{ r_plugins_from_github | default([]) }}'
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github' ]
ignore_errors: True
- name: Install R packages 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 if (packageVersion('{{ item.name }}') != '{{ item.version }}') { install.packages('{{ r_source_plugins_dest_dir }}/{{ item.source }}', repos = NULL, type='source'); print('Added'); } else { print('Already Installed'); }"
register: install_v_plugins_result
failed_when: "install_v_plugins_result.rc != 0 or 'had non-zero exit status' in install_v_plugins_result.stderr"
changed_when: '"Added" in install_s_plugins_result.stdout'
with_items: '{{ r_plugins_from_sources | default([]) }}'
ignore_errors: True
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
- name: Remove R unwanted packages
command: >
Rscript --slave --no-save --no-restore-history -e "if (! ('{{ item }}' %in% installed.packages()[,'Package'])) { print('Not installed'); } else { remove.packages(pkgs='{{ item }}'); print('Removed'); }"
register: remove_plugins_result
failed_when: remove_plugins_result.rc != 0
changed_when: "'Removed' in remove_plugins_result.stdout"
with_items: '{{ r_plugins_list_to_remove | default([]) }}'
when: r_plugins_list_to_remove is defined
tags: [ 'r_software', 'r_pkg', 'r_plugins' ]

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tasks/r-packages-updater.yml Normal file
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---
- block:
- name: Install the R packages updater script
template:
src: 'update_r_packages.sh.j2'
dest: '/usr/local/bin/update_r_packages'
owner: root
group: root
mode: '0755'
- name: Create the R packages updater SVN base directory
file:
dest: '{{ r_packages_svn_base_dir }}'
state: directory
- name: Cron job that installs new R packages, if any
cron:
name: "install new R packages"
user: root
cron_file: install-r-packages
minute: "*/10"
hour: "5-23,1-2"
job: "/usr/local/bin/update_r_packages install >/var/log/install_r_packages 2>&1"
state: present
- name: Cron job that upgrades existing R packages and installs new ones, if any
cron:
name: "Upgrade installed R packages"
user: root
cron_file: upgrade-r-packages
minute: "7"
hour: "3"
job: "/usr/local/bin/update_r_packages upgrade >/var/log/update_r_packages 2>&1"
state: present
when: r_packages_updater_also_upgrades_installed_packages
when: r_packages_updater
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github', 'r_cran_pkgs', 'r_github_pkgs', 'r_packages_updater' ]
- block:
- name: Remove the R packages updater script
file: dest=/usr/local/bin/update_r_packages state=absent
- name: Remove the R packages updater SVN base directory
file: dest={{ r_packages_svn_base_dir }} state=absent
- name: Remove the cron job that installs new R packages
file: dest=/etc/cron.d/install-r-packages state=absent
- name: Remove the cron job that upgrades existing R packages and installs new ones
file: dest=/etc/cron.d/upgrade-r-packages state=absent
when: not r_packages_updater
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github', 'r_cran_pkgs', 'r_github_pkgs', 'r_packages_updater' ]
- block:
- name: Disable the cron job that upgrades already installed R packages
file: dest=/etc/cron.d/upgrade-r-packages state=absent
when: not r_packages_updater_also_upgrades_installed_packages
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github', 'r_cran_pkgs', 'r_github_pkgs', 'r_packages_updater' ]

8
tasks/r-packages_cleanup.yml Normal file
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---
- name: Install the script that cleans up the R deb and cran packages
copy: src=r_packages_cleanup.sh dest=/usr/local/bin/r_packages_cleanup owner=root group=root mode=0500
tags: [ 'r_software', 'r_pkgs', 'r_cleanup' ]
- name: Remove all the old R deb and cran packages. Otherwise the upgrade will fail miserably
shell: /usr/local/bin/r_packages_cleanup
tags: [ 'r_software', 'r_pkgs', 'r_cleanup' ]

22
templates/Rprofile.site.j2 Normal file
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## Emacs please make this -*- R -*-
## empty Rprofile.site for R on Debian
##
## Copyright (C) 2008 Dirk Eddelbuettel and GPL'ed
##
## see help(Startup) for documentation on ~/.Rprofile and Rprofile.site
#
# NOTE: managed by ansible
#
local({r <- getOption("repos")
r["CRAN"] <- "{{ r_cran_mirror_site }}"
options(repos=r)
})
# Explicitly set the R encoding using the system one, if it exists
if (file.exists("/etc/default/locale")) {
readRenviron("/etc/default/locale")
LANG <- Sys.getenv("LANG")
if(nchar(LANG))
Sys.setlocale("LC_ALL", LANG)
}

298
templates/update_r_packages.sh.j2 Normal file
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#!/bin/bash
#
# TODO: kill an old process if it is running from too much time (12 hours?)
# using something like ps -o etimes= -p "$PROCNUM"
#
export PATH="$PATH:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin"
RETVAl=
PARAMS=$#
ACTION=$1
PROCNUM=$$
OLDPROC=
OLDPROC_RUNNING=
LOCKDIR=/var/run
LOCK_FILE=$LOCKDIR/.update_r_pkgs.lock
TMP_FILES_DIR=/var/tmp/r_pkgs_update
# We cannot answer questions
DEBIAN_FRONTEND=noninteractive
R_CRAN_MIRROR="{{ r_cran_mirror_site }}"
R_PKGS_FROM_SVN="{{ r_package_updater_via_subversion }}"
R_PKGS_SVN_DIR=RPackagesManagement
R_PKGS_SVN_URL="{{ r_package_updater_subversion_repo }}"
R_PKGS_SVN_BASE_DIR="{{ r_packages_svn_base_dir }}"
R_PKGS_FILES_PREFIX="{{ r_packages_svn_files_prefix }}"
RSCRIPT_OPTIONS="--slave --no-site-file --no-init-file --no-save --no-restore-history"
SVN_UPDATE_STATUS=
# In seconds. 60*60*6=21600s (6h)
UPDATER_PROCESS_MAX_RUNTIME=21600
# - debian packages list format:
# one package per line
DEB_PKGS_SKIP=0
DEBIAN_PKGS_LIST_URL="{{ r_debian_packages_list_url | default('') }}"
EL_PKGS_LIST_URL="{{ r_el_packages_list_url | default('') }}"
PKGS_LIST=
# - R packages list format:
# name[:mirror]
CRAN_PKGS_SKIP=0
R_PKGS_LIST_URL="{{ r_cran_packages_list_url | default('') }}"
R_PKGS_LIST=
# - R versioned packages list format:
# name:version
CRAN_VERSIONED_PKGS_SKIP=0
R_VERSIONED_PKGS_LIST_URL="{{ r_cran_versioned_packages_list_url | default('') }}"
R_VERSIONED_PKGS_LIST=
# - R packages from github list format:
# - owner/package
GITHUB_PKGS_SKIP=0
R_PKGS_FROM_GITHUB_LIST_URL="{{ r_github_packages_list_url | default('') }}"
R_PKGS_GITHUB=
trap "logger 'update_r_packages: trap intercepted, exiting.' ; cleanup" SIGHUP SIGINT SIGTERM
function cleanup() {
logger "update_r_packages: cleaning up"
rm -f $LOCK_FILE
rm -fr $TMP_FILES_DIR
}
function usage() {
if [ $PARAMS -ne 1 ] ; then
echo "Need at least an argument: 'upgrade' or 'install'."
echo "- 'upgrade' installs new packages and upgrades the existin ones when needed."
echo "- 'install' installs new packages."
cleanup
exit 1
fi
}
function get_args() {
if [ "$ACTION" != "upgrade" -a "$ACTION" != "install" ] ; then
usage
fi
}
function fail() {
logger "update_r_packages: Something went wrong, exiting."
cleanup
exit 1
}
function init_env() {
if [ -f $LOCK_FILE ] ; then
OLDPROC=$( cat $LOCK_FILE )
OLDPROC_RUNNING=$( ps auwwx | grep -v grep | grep $OLDPROC | awk '{ print $2 }' )
RETVAL=$?
if [ ! -z "$OLDPROC_RUNNING" ] ; then
logger "update_r_packages: pid of the already running process: $OLDPROC_RUNNING"
OLDPROC_RUNNING_TIME=$( ps -o etimes= -p ${OLDPROC_RUNNING} )
if [ $OLDPROC_RUNNING_TIME -gt $UPDATER_PROCESS_MAX_RUNTIME ] ; then
logger "update_r_packages: process $OLDPROC_RUNNING was running for $OLDPROC_RUNNING_TIME seconds. Got stuck, killing it"
kill -9 $OLDPROC_RUNNING
cleanup
else
logger "update_r_packages: another process is running, exiting."
exit 0
fi
else
logger "update_r_packages: lock file exist but the process not. Continuing."
rm -fr $TMP_FILES_DIR
fi
else
logger 'update_r_packages: no other jobs running, proceeding.'
fi
RETVAL=
echo "$PROCNUM" > $LOCK_FILE
mkdir -p $TMP_FILES_DIR
}
function get_data_files() {
logger "update_r_packages: get the single files from http."
# Get the packages list
if [ -z $DEBIAN_PKGS_LIST_URL ] ; then
DEB_PKGS_SKIP=1
logger "update_r_packages: the debian packages list is not available."
else
PKGS_LIST=$( mktemp $TMP_FILES_DIR/rdebs.XXXXXXX )
logger "update_r_packages: getting the debian packages list."
wget -q -o /dev/null -O $PKGS_LIST $DEBIAN_PKGS_LIST_URL
fi
if [ -z $R_PKGS_LIST_URL ] ; then
CRAN_PKGS_SKIP=1
logger "update_r_packages: the CRAN packages list is not available."
else
R_PKGS_LIST=$( mktemp $TMP_FILES_DIR/rpkgs.XXXXXXX )
logger "update_r_packages: getting the R packages list that will be installed from CRAN"
wget -q -o /dev/null -O $R_PKGS_LIST $R_PKGS_LIST_URL
fi
if [ -z $R_VERSIONED_PKGS_LIST_URL ] ; then
CRAN_VERSIONED_PKGS_SKIP=1
logger "update_r_packages: the CRAN versioned packages list is not available."
else
R_PKGS_LIST=$( mktemp $TMP_FILES_DIR/rpkgs.XXXXXXX )
logger "update_r_packages: getting the R versioned packages list that will be installed from CRAN"
wget -q -o /dev/null -O $R_VERSIONED_PKGS_LIST $R_VERSIONED_PKGS_LIST_URL
fi
if [ -z $R_PKGS_FROM_GITHUB_LIST_URL ] ; then
GITHUB_PKGS_SKIP=1
logger "update_r_packages: the Github packages list is not available."
else
R_PKGS_GITHUB=$( mktemp $TMP_FILES_DIR/rpkgsgithub.XXXXXXX )
logger "update_r_packages: getting the R packages list that will be installed from github"
wget -q -o /dev/null -O $R_PKGS_GITHUB $R_PKGS_FROM_GITHUB_LIST_URL
fi
}
function get_data_files_from_svn() {
logger "update_r_packages: files from a SVN repo."
if [ -d $R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR ] ; then
logger "update_r_packages: SVN update"
cd $R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR
SVN_CLEANUP_OP=$( svn cleanup )
SVN_UPDATE_OP=$( svn update | tail -1 | grep Updated >/dev/null 2>&1 )
SVN_UPDATE_STATUS=$?
else
cd $R_PKGS_SVN_BASE_DIR
logger "update_r_packages: first SVN checkout."
svn co $R_PKGS_SVN_URL >/dev/null 2>&1
fi
PKGS_LIST=$R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR/${R_PKGS_FILES_PREFIX}r_deb_pkgs.txt
R_PKGS_LIST=$R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR/${R_PKGS_FILES_PREFIX}r_cran_pkgs.txt
R_VERSIONED_PKGS_LIST=$R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR/${R_PKGS_FILES_PREFIX}r_cran_versioned_pkgs.txt
R_PKGS_GITHUB=$R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR/${R_PKGS_FILES_PREFIX}r_github_pkgs.txt
}
{% if ansible_distribution_file_variety == "Debian" %}
function distribution_pkgs() {
if [ $DEB_PKGS_SKIP -eq 0 ] ; then
# Update the apt cache and install the packages in non interactive mode
logger "update_r_packages: Installing the debian dependencies"
if [ -z "$(find /var/cache/apt/pkgcache.bin -mmin -360)" ]; then
apt-get update -q >/dev/null 2>&1
else
logger "update_r_packages: APT cache not updated"
fi
>/var/log/update_r_debs.log
while read deb_pkg ; do
apt-get install ${deb_pkg} -q -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" >>/var/log/update_r_debs.log 2>&1
done < $PKGS_LIST
apt-get autoremove -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" >> /var/log/update_r_debs.log 2>&1
else
logger "update_r_packages: skipping the debian packages installation"
fi
}
function remove_r_install_packages_lock_files() {
# install.packages leaves lock files around if the process crashes
rm -fr {{ r_sitelib_path }}/00LOCK-*
}
{% endif %}
{% if ansible_distribution_file_variety == "RedHat" %}
function distribution_pkgs() {
if [ $EL_PKGS_SKIP -eq 0 ] ; then
# Update the apt cache and install the packages in non interactive mode
logger "update_r_packages: Installing the EL dependencies"
if [ -z "$(find /var/cache/apt/pkgcache.bin -mmin -360)" ]; then
apt-get update -q >/dev/null 2>&1
else
logger "update_r_packages: APT cache not updated"
fi
>/var/log/update_r_debs.log
while read el_pkg ; do
yum -y install ${el_pkg} >>/var/log/update_r_el.log 2>&1
done < $PKGS_LIST
else
logger "update_r_packages: skipping the EL packages installation"
fi
}
function remove_r_install_packages_lock_files() {
# install.packages leaves lock files around if the process crashes
rm -fr {{ r_sitelib_path }}/00LOCK-*
}
{% endif %}
function r_cran_pkgs() {
if [ $CRAN_PKGS_SKIP -eq 0 ] ; then
logger "update_r_packages: Installing R packages from CRAN"
for l in $( cat $R_PKGS_LIST ) ; do
pkg=$( echo $l | cut -d : -f 1 )
is_mirror_ret=
is_mirror=$( echo $l | grep ':' )
is_mirror_ret=$?
if [ $is_mirror_ret -eq 0 ] ; then
mirror=$( echo $l | cut -d : -f 2- )
else
mirror=$R_CRAN_MIRROR
fi
if [ "$ACTION" == "upgrade" ] ; then
Rscript $RSCRIPT_OPTIONS -e "install.packages(pkgs='$pkg', repos=c('$mirror/'));"
else
Rscript $RSCRIPT_OPTIONS -e "if (! ('$pkg' %in% installed.packages()[,'Package'])) { install.packages(pkgs='$pkg', repos=c('$mirror/')); }"
fi
done
else
logger "update_r_packages: skipping the R CRAN packages installation"
fi
}
function r_cran_versioned_pkgs() {
if [ $CRAN_VERSIONED_PKGS_SKIP -eq 0 ] ; then
logger "update_r_packages: Installing versioned R packages from CRAN"
for l in $( cat $R_VERSIONED_PKGS_LIST ) ; do
pkg=$( echo $l | cut -d : -f 1 )
version=$( echo $l | cut -d : -f 2 )
if [ "$ACTION" == "upgrade" ] ; then
Rscript $RSCRIPT_OPTIONS -e "require(devtools); install_version('$pkg', '$version', repos=c('$mirror/'));"
else
Rscript $RSCRIPT_OPTIONS -e "if (! ('$pkg' %in% installed.packages()[,'Package'])) { require(devtools); install_version('$pkg', '$version', repos=c('$mirror/')); }"
fi
done
else
logger "update_r_packages: skipping the R CRAN versioned packages installation"
fi
}
function r_github_pkgs() {
if [ $GITHUB_PKGS_SKIP -eq 0 ] ; then
logger "update_r_packages: Installing R packages from Github"
for l in $( cat $R_PKGS_GITHUB ) ; do
pkg=$( echo $l | cut -d "/" -f 2 )
if [ "$ACTION" == "upgrade" ] ; then
Rscript --slave --no-save --no-restore-history -e "require(devtools); require(methods); require(jsonlite) ; package_to_install <- '$l' ; refs <- jsonlite::read_json(sprintf('https://api.github.com/repos/%s/releases', package_to_install)) ; ref_to_install <- 'master'; if(length(refs)>0) { ref_to_install <- refs[[1]][['tag_name']] } ; devtools::install_github(package_to_install, ref = ref_to_install, upgrade='always')"
else
Rscript --slave --no-save --no-restore-history -e "if (! ('$pkg' %in% installed.packages()[,'Package'])) { require(devtools); require(methods); require(jsonlite) ; package_to_install <- '$l' ; refs <- jsonlite::read_json(sprintf('https://api.github.com/repos/%s/releases', package_to_install)) ; ref_to_install <- 'master'; if(length(refs)>0) { ref_to_install <- refs[[1]][['tag_name']] } ; devtools::install_github(package_to_install, ref = ref_to_install, upgrade='always') }"
fi
done
else
logger "update_r_packages: skipping the R GitHub packages installation"
fi
}
#########
# Main
#
usage
get_args
init_env
if [ $R_PKGS_FROM_SVN == 'True' ] ; then
get_data_files_from_svn
if [ $SVN_UPDATE_STATUS -ne 0 -a "$ACTION" == "install" ] ; then
logger "update_r_packages: nothing new to install from SVN, exiting"
cleanup
exit 0
fi
else
get_data_files
fi
distribution_pkgs
remove_r_install_packages_lock_files
r_cran_pkgs
r_cran_versioned_pkgs
r_github_pkgs
cleanup
exit 0

2
vars/main.yml
View File

@ -1,2 +1,2 @@
---
# vars file for ansible-role-template
centos_install_epel: true