New way to stick to a specific version of R.
This commit is contained in:
parent
4aad1fb00e
commit
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GPG Key ID:
147ABE6CEB9E20FF
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@ -10,7 +10,7 @@
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# The install/remove script has been taken from here: http://adamj.eu/tech/2014/07/19/installing-and-removing-r-packages-with-ansible/
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#
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# Set to True if you want install from the CRAN deb repository
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r_install_cran_repo: False
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r_install_cran_repo: false
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# This si the CRAN main repository, that contains the r-base-* packages
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r_cran_ubuntu_repo_key: 'E298A3A825C0D65DFD57CBB651716619E084DAB9'
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r_cran_ubuntu_repo: 'deb https://cloud.r-project.org/bin/linux/ubuntu {{ ansible_distribution_release }}-cran40/'
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@ -25,27 +25,25 @@ r_apt_additional_repos:
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- 'ppa:ubuntugis/ppa'
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- 'ppa:cran/libgit2'
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r_cran_set_default_mirror: True
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r_cran_set_default_mirror: true
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r_cran_mirror_site: https://cran.mirror.garr.it/mirrors/CRAN/
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r_base_specific_version: False
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r_base_pkg_version: 4.1.0
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r_packages_main_state: present
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r_packages_state: '{{ r_packages_main_state }}'
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r_base_versioned: false
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r_base_pkg_version: 4.2.3-1.1804.0
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r_sitelib_path: '/usr/local/lib/R/site-library'
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r_plugins_from_deb: True
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r_packages_cleanup: False
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r_install_rprofile_site: True
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r_plugins_from_deb: true
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r_packages_cleanup: false
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r_install_rprofile_site: true
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#
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r_packages_updater: True
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r_package_updater_via_subversion: False
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r_packages_updater: true
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r_package_updater_via_subversion: false
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r_package_updater_subversion_repo: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/
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r_packages_svn_base_dir: /srv/r_updater
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r_package_updater_via_git: True
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r_package_updater_via_git: true
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r_package_updater_git_repo: 'https://code-repo.d4science.org/gCubeSystem/r-packages-list'
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r_packages_git_base_dir: /srv/r_updater
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r_packages_files_prefix: ''
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r_packages_updater_also_upgrades_installed_packages: True
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r_packages_updater_for_github_only: True
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r_packages_updater_also_upgrades_installed_packages: true
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r_packages_updater_for_github_only: true
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# They need to be flat text files
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# 1 package per line
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#r_debian_packages_list_url
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@ -67,6 +65,13 @@ r_base_packages_list:
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- r-base-html
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- r-mathlib
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r_base_versioned_packages_list:
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# - r-base=4.2.3-1.1804.0 # r-recommended is a requirement and it cannot be installed
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- "r-base-core={{ r_base_pkg_version }}"
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- "r-base-dev={{ r_base_pkg_version }}"
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- "r-base-html={{ r_base_pkg_version }}"
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- "r-mathlib={{ r_base_pkg_version }}"
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r_distribution_required_packages:
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- jags
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- git
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@ -89,8 +94,12 @@ r_distribution_required_packages:
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- libnetcdf-dev
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- netcdf-bin
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# Some packages must be put on hold
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# Some packages that must be put on hold
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r_base_packages_hold_list: []
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# - r-base-core
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# - r-base-dev
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# - r-base-html
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# - r-mathlib
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r_plugins_packages_list: []
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@ -215,7 +224,6 @@ r_cran_ubuntu_packages:
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- r-cran-rpart
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- r-cran-rprojroot
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- r-cran-rsconnect
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- r-cran-rstan
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- r-cran-rstanarm
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- r-cran-rstantools
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- r-cran-rstudioapi
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@ -1,14 +1,11 @@
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galaxy_info:
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author: Andrea Dell'Amico
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description: Systems Architect
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description: ansible role that installs R and a list of R packages from CRAN or any other repositories
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company: ISTI-CNR
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issue_tracker_url: https://redmine-s2i2s.isti.cnr.it/projects/provisioning
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namespace: adellam
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role_name: r_distribution
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license: EUPL 1.2+
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min_ansible_version: 2.8
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min_ansible_version: "2.14"
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# To view available platforms and versions (or releases), visit:
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# https://galaxy.ansible.com/api/v1/platforms/
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#
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@ -16,10 +13,8 @@ galaxy_info:
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- name: Ubuntu
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versions:
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- bionic
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- name: EL
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versions:
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- 7
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- focal
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- jammy
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galaxy_tags:
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- R
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- CRAN
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@ -1,101 +1,117 @@
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---
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- block:
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- name: Add the CRAN repository (Ubuntu Trusty PPA)
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apt_repository:
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repo: '{{ r_cran_ubuntu_packages_ppa_trusty }}'
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state: present
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update_cache: yes
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- name: Install some additional repositories. They provide dependencies for some R packages. Ubuntu Bionic
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apt_repository:
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repo: '{{ item }}'
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state: present
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update_cache: yes
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loop: '{{ r_apt_additional_repos_trusty }}'
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- name: r-installation-deb | Manage the CRAN PPA
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when:
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- r_install_cran_repo
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- ansible_distribution_version is version_compare('14.04', '==')
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tags: ['r_software', 'r_repo']
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- block:
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- name: Install the CRAN main R repository key
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apt_key:
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keyserver: 'keyserver.ubuntu.com'
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id: '{{ r_cran_ubuntu_repo_key }}'
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- name: Install the CRAN main R repository
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apt_repository:
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repo: '{{ r_cran_ubuntu_repo }}'
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block:
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- name: r-installation-deb | Add the CRAN repository (Ubuntu Trusty PPA)
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ansible.builtin.apt_repository:
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repo: '{{ r_cran_ubuntu_packages_ppa_trusty }}'
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state: present
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update_cache: yes
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update_cache: true
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- name: Add the CRAN repository (Ubuntu Bionic PPA)
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apt_repository:
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repo: '{{ r_cran_ubuntu_packages_ppa }}'
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state: present
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update_cache: yes
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- name: Install some additional repositories. They provide dependencies for some R packages. Ubuntu Bionic
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apt_repository:
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- name: r-installation-deb | Install some additional repositories. They provide dependencies for some R packages. Ubuntu Bionic
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ansible.builtin.apt_repository:
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repo: '{{ item }}'
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state: present
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update_cache: yes
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loop: '{{ r_apt_additional_repos }}'
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update_cache: true
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loop: '{{ r_apt_additional_repos_trusty }}'
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- name: r-installation-deb | Manage the CRAN PPA on Ubuntu >= 16.04
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when:
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- r_install_cran_repo
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- ansible_distribution_version is version_compare('18.04', '>=')
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tags: ['r_software', 'r_repo']
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block:
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- name: r-installation-deb | Install the CRAN main R repository key
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ansible.builtin.apt_key:
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keyserver: 'keyserver.ubuntu.com'
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id: '{{ r_cran_ubuntu_repo_key }}'
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- block:
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- name: Remove the CRAN repositores
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apt_repository:
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repo: '{{ r_cran_ubuntu_packages_ppa }}'
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state: absent
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update_cache: yes
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- name: Remove the CRAN main repository
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apt_repository:
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- name: r-installation-deb | Install the CRAN main R repository
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ansible.builtin.apt_repository:
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repo: '{{ r_cran_ubuntu_repo }}'
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state: absent
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update_cache: yes
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state: present
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update_cache: true
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- name: r-installation-deb | Add the CRAN repository (Ubuntu Bionic PPA)
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ansible.builtin.apt_repository:
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repo: '{{ r_cran_ubuntu_packages_ppa }}'
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state: present
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update_cache: true
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- name: r-installation-deb | Install some additional repositories. They provide dependencies for some R packages. Ubuntu Bionic
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ansible.builtin.apt_repository:
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repo: '{{ item }}'
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state: present
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update_cache: true
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loop: '{{ r_apt_additional_repos }}'
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- name: r-installation-deb | Remove the CRAN repo when we do not want it
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when: not r_install_cran_repo
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tags: ['r_software', 'r_repo']
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block:
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- name: r-installation-deb | Remove the CRAN repositores
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ansible.builtin.apt_repository:
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repo: '{{ r_cran_ubuntu_packages_ppa }}'
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state: absent
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update_cache: true
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- block:
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- name: Remove the hold state from the debian R packages
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shell: apt-mark unhold {{ item }}
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- name: r-installation-deb | Remove the CRAN main repository
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ansible.builtin.apt_repository:
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repo: '{{ r_cran_ubuntu_repo }}'
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state: absent
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update_cache: true
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- name: r-installation-deb | Install the R base packages from the repository, unversioned
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when: not r_base_versioned
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tags: ['r_software', 'r_pkg', r_unversioned_packages]
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block:
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- name: r-installation-deb | Remove the hold state from the debian R packages
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ansible.builtin.dpkg_selections:
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name: "{{ item }}"
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selection: install
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with_items: '{{ r_base_packages_hold_list | default([]) }}'
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when: r_base_packages_hold_list is defined
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ignore_errors: True
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tags: ['r_software', 'r_pkg', 'r_pkg_hold']
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- name: Install the R base packages.
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apt:
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- name: r-installation-deb | Install the R base packages.
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ansible.builtin.apt:
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pkg: '{{ r_base_packages_list }}'
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state: '{{ r_packages_main_state }}'
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state: present
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cache_valid_time: 3600
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- name: When we install specific R deb packages, put them on hold
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shell: apt-mark hold {{ item }}
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- name: r-installation-deb | Install the R base packages from the repository, versioned. Put them on hold
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when: r_base_versioned
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tags: ['r_software', 'r_pkg', r_unversioned_packages]
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block:
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- name: r-installation-deb | Install the R base packages, versioned.
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ansible.builtin.apt:
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pkg: '{{ r_base_versioned_packages_list }}'
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state: present
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cache_valid_time: 3600
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- name: r-installation-deb | Put some packages into hold state
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ansible.builtin.dpkg_selections:
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name: "{{ item }}"
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selection: hold
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with_items: '{{ r_base_packages_hold_list | default([]) }}'
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when: r_base_specific_version
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ignore_errors: True
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tags: ['r_software', 'r_pkg', 'r_pkg_hold']
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- name: Install the R additional modules from the deb repo
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apt:
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- name: r-installation-deb | Manage additional packages
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tags: ['r_software', 'r_pkg', r_unversioned_packages]
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block:
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- name: r-installation-deb | Install some additional R modules from the deb repo
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ansible.builtin.apt:
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pkg: '{{ r_plugins_packages_list }}'
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state: '{{ r_packages_state }}'
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cache_valid_time: 3600
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- name: Install some packages needed by R packages when installed from source
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apt:
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- name: r-installation-deb | Install some packages required by R packages when installed from source
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ansible.builtin.apt:
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pkg: '{{ r_distribution_required_packages }}'
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state: '{{ r_packages_state }}'
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cache_valid_time: 3600
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tags: ['r_software', 'r_pkg', 'r_deps']
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tags: [ 'r_software', 'r_pkg' ]
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