forked from ISTI-ansible-roles/ansible-roles
d4science-ghn-cluster: New dataminer version and R packages list.
library/roles/R: A script that remove the old R installation, on demand.
This commit is contained in:
Andrea Dell'Amico
parent
c8645263ce
commit
4662445ea7
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@ -21,6 +21,7 @@ r_needs_additional_distro_pkgs: False
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r_plugins_from_deb: True
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r_plugins_from_deb: True
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r_plugins_install_latest_source: True
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r_plugins_install_latest_source: True
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r_plugins_install_specific_source: True
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r_plugins_install_specific_source: True
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r_packages_cleanup: False
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r_source_plugins_dest_dir: /var/cache/R
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r_source_plugins_dest_dir: /var/cache/R
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@ -0,0 +1,13 @@
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#!/bin/bash
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# Put the base packages to unhold
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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
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# Remove the old r packages
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apt-get purge r-base-* r-cran-* -y
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# Remove the CRAN packages
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rm -fr /usr/lib/R /usr/local/lib/R
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rm -fr /var/cache/R/*
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exit 0
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108
R/tasks/main.yml
108
R/tasks/main.yml
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@ -1,106 +1,4 @@
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---
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---
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- name: Manage the cran repository key
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- include: r-packages_cleanup.yml
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apt_key: id=E084DAB9 keyserver=keyserver.ubuntu.com state={{ r_install_cran_repo }}
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when: r_packages_cleanup
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tags: [ 'r_software', 'r_repo' ]
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- include: r-installation.yml
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- name: Manage the cran repository definition
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apt_repository: repo='deb http://cran.rstudio.com/bin/linux/ubuntu {{ ansible_distribution_release }}/' state={{ r_install_cran_repo }} update_cache=yes
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tags: [ 'r_software', 'r_repo' ]
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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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with_items: r_base_packages_hold_list
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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: pkg={{ item }} state={{ r_packages_main_state }} force=yes
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with_items: r_base_packages_list
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tags: [ 'r_software', 'r_pkg' ]
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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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with_items: r_base_packages_hold_list
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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: pkg={{ item }} state={{ r_packages_state }} force=yes
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with_items: r_plugins_packages_list
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when: r_plugins_from_deb
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tags: [ 'r_software', 'r_pkg' ]
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- name: Configure the default CRAN mirror
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template: src=Rprofile.site.j2 dest=/etc/R/Rprofile.site owner=root group=root mode=0444
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when: r_install_cran_repo == 'present'
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tags: [ 'r_software', 'r_profile', 'r_pkg' ]
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- name: Install some packages needed by R packages when installed from source
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apt: pkg={{ item }} state={{ r_packages_state }} update_cache=yes force=yes
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with_items: r_distribution_required_packages
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when: r_needs_additional_distro_pkgs
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tags: [ 'r_software', 'r_pkg' ]
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- name: Ensure that the R packages sources directory exists
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file: dest={{ r_source_plugins_dest_dir }} state=directory owner=root group=root
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when: r_plugins_from_sources is defined
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
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- name: Install R packages from the cran sources repo, latest available version
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command: >
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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'); }"
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register: install_plugins_result
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failed_when: "install_plugins_result.rc != 0 or 'had non-zero exit status' in install_plugins_result.stderr"
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changed_when: "'Added' in install_plugins_result.stdout"
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with_items: r_plugins_list_to_install
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when: r_plugins_install_latest_source
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tags: [ 'r_software', 'r_pkg', 'r_plugins' ]
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- name: Get the R packages sources that need to be installed
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get_url: url={{ item.url }} dest={{ r_source_plugins_dest_dir }}
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with_items: r_plugins_from_sources
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when: r_plugins_install_specific_source
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
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- name: Install R packages from the cran sources, specific versions
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command: >
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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'); }"
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register: install_s_plugins_result
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failed_when: "install_s_plugins_result.rc != 0 or 'had non-zero exit status' in install_s_plugins_result.stderr"
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changed_when: '"Added" in install_s_plugins_result.stdout'
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with_items: r_plugins_from_sources
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when: r_plugins_install_specific_source
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ignore_errors: True
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
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- name: Install R packages from the cran sources, specific versions. Second round, to avoid circular dependencies
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command: >
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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'); }"
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register: install_s_plugins_result
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failed_when: "install_s_plugins_result.rc != 0 or 'had non-zero exit status' in install_s_plugins_result.stderr"
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changed_when: '"Added" in install_s_plugins_result.stdout'
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with_items: r_plugins_from_sources
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when: r_plugins_install_specific_source
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
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- name: Install R packages from github
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command: >
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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'); }"
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register: install_github_plugins_result
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failed_when: "install_github_plugins_result.rc != 0 or 'had non-zero exit status' in install_github_plugins_result.stderr"
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changed_when: "'Added' in install_github_plugins_result.stdout"
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with_items: r_plugins_from_github
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when: r_plugins_from_github is defined
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github' ]
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- name: Remove R unwanted packages
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command: >
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Rscript --slave --no-save --no-restore-history -e "if (! ('{{ item }}' %in% installed.packages()[,'Package'])) { print('Not installed'); } else { remove.packages(pkgs='{{ item }}'); print('Removed'); }"
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register: remove_plugins_result
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failed_when: remove_plugins_result.rc != 0
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changed_when: "'Removed' in remove_plugins_result.stdout"
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with_items: r_plugins_list_to_remove
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when: r_plugins_list_to_remove is defined
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tags: [ 'r_software', 'r_pkg', 'r_plugins' ]
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@ -0,0 +1,106 @@
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---
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- name: Manage the cran repository key
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apt_key: id=E084DAB9 keyserver=keyserver.ubuntu.com state={{ r_install_cran_repo }}
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tags: [ 'r_software', 'r_repo' ]
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- name: Manage the cran repository definition
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apt_repository: repo='deb http://cran.rstudio.com/bin/linux/ubuntu {{ ansible_distribution_release }}/' state={{ r_install_cran_repo }} update_cache=yes
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tags: [ 'r_software', 'r_repo' ]
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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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with_items: r_base_packages_hold_list
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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: pkg={{ item }} state={{ r_packages_main_state }} force=yes
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with_items: r_base_packages_list
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tags: [ 'r_software', 'r_pkg' ]
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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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with_items: r_base_packages_hold_list
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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: pkg={{ item }} state={{ r_packages_state }} force=yes
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with_items: r_plugins_packages_list
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when: r_plugins_from_deb
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tags: [ 'r_software', 'r_pkg' ]
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- name: Configure the default CRAN mirror
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template: src=Rprofile.site.j2 dest=/etc/R/Rprofile.site owner=root group=root mode=0444
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when: r_install_cran_repo == 'present'
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tags: [ 'r_software', 'r_profile', 'r_pkg' ]
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- name: Install some packages needed by R packages when installed from source
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apt: pkg={{ item }} state={{ r_packages_state }} update_cache=yes force=yes
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with_items: r_distribution_required_packages
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when: r_needs_additional_distro_pkgs
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tags: [ 'r_software', 'r_pkg' ]
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- name: Ensure that the R packages sources directory exists
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file: dest={{ r_source_plugins_dest_dir }} state=directory owner=root group=root
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when: r_plugins_from_sources is defined
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
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- name: Install R packages from the cran sources repo, latest available version
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command: >
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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'); }"
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register: install_plugins_result
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failed_when: "install_plugins_result.rc != 0 or 'had non-zero exit status' in install_plugins_result.stderr"
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changed_when: "'Added' in install_plugins_result.stdout"
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with_items: r_plugins_list_to_install
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when: r_plugins_install_latest_source
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tags: [ 'r_software', 'r_pkg', 'r_plugins' ]
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- name: Get the R packages sources that need to be installed
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get_url: url={{ item.url }} dest={{ r_source_plugins_dest_dir }}
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with_items: r_plugins_from_sources
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when: r_plugins_install_specific_source
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
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- name: Install R packages from the cran sources, specific versions
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command: >
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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'); }"
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register: install_s_plugins_result
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failed_when: "install_s_plugins_result.rc != 0 or 'had non-zero exit status' in install_s_plugins_result.stderr"
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changed_when: '"Added" in install_s_plugins_result.stdout'
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with_items: r_plugins_from_sources
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when: r_plugins_install_specific_source
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ignore_errors: True
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
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- name: Install R packages from the cran sources, specific versions. Second round, to avoid circular dependencies
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command: >
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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'); }"
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register: install_s_plugins_result
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failed_when: "install_s_plugins_result.rc != 0 or 'had non-zero exit status' in install_s_plugins_result.stderr"
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changed_when: '"Added" in install_s_plugins_result.stdout'
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with_items: r_plugins_from_sources
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when: r_plugins_install_specific_source
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
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- name: Install R packages from github
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command: >
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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'); }"
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register: install_github_plugins_result
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failed_when: "install_github_plugins_result.rc != 0 or 'had non-zero exit status' in install_github_plugins_result.stderr"
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changed_when: "'Added' in install_github_plugins_result.stdout"
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with_items: r_plugins_from_github
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when: r_plugins_from_github is defined
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github' ]
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- name: Remove R unwanted packages
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command: >
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Rscript --slave --no-save --no-restore-history -e "if (! ('{{ item }}' %in% installed.packages()[,'Package'])) { print('Not installed'); } else { remove.packages(pkgs='{{ item }}'); print('Removed'); }"
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register: remove_plugins_result
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failed_when: remove_plugins_result.rc != 0
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changed_when: "'Removed' in remove_plugins_result.stdout"
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with_items: r_plugins_list_to_remove
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when: r_plugins_list_to_remove is defined
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tags: [ 'r_software', 'r_pkg', 'r_plugins' ]
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@ -0,0 +1,8 @@
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---
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- name: Install the script that cleans up the R deb and cran packages
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copy: src=r_packages_cleanup.sh dest=/usr/local/bin/r_packages_cleanup owner=root group=root mode=0500
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tags: [ 'r_software', 'r_pkgs', 'r_cleanup' ]
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- name: Remove all the old R deb and cran packages. Otherwise the upgrade will fail miserably
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shell: /usr/local/bin/r_packages_cleanup
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tags: [ 'r_software', 'r_pkgs', 'r_cleanup' ]
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