CRAN PPA for R 4.0+, git listfiles.

2021-07-02 15:52:58 +02:00 · 2021-07-02 15:52:58 +02:00 · 23f78b67a0
parent 97d779e028
commit 23f78b67a0
6 changed files with 327 additions and 126 deletions
--- a/defaults/main.yml
+++ b/defaults/main.yml
@ -11,18 +11,20 @@
 #
 # Set to True if you want install from the CRAN deb repository
 r_install_cran_repo: False
-# “Michael Rutter marutter@gmail.com” with key ID 0x51716619e084dab9
-# E298A3A825C0D65DFD57CBB651716619E084DAB9
-r_cran_repo_apt_key: 'E298A3A825C0D65DFD57CBB651716619E084DAB9'
-# Use 'cran35' for R 3.6
-r_cran_repo_version: 'cran40'
-r_cran_repo_url: 'https://cloud.r-project.org/bin/linux/ubuntu {{ ansible_distribution_release }}-{{ r_cran_repo_version }}/'
 # Use 'marutter/c2d4u3.5' for R 3.6
-r_cran_ubuntu_packages_ppa: 'ppa:marutter/c2d4u'
+r_cran_ubuntu_packages_ppa_trusty: 'ppa:marutter/c2d4u'
+# 4.1, Ubuntu 18.04+
+r_cran_ubuntu_packages_ppa: 'ppa:c2d4u.team/c2d4u4.0+'
+r_apt_additional_repos_trusty:
+  - 'ppa:opencpu/jq'
+r_apt_additional_repos:
+  - 'ppa:cran/v8'
+  - 'ppa:ubuntugis/ppa'
+
 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: 4.0.3
+r_base_pkg_version: 4.1.0
 r_packages_main_state: present
 r_packages_state: '{{ r_packages_main_state }}'
 r_sitelib_path: '/usr/local/lib/R/site-library'
@ -30,10 +32,13 @@ r_plugins_from_deb: True
 r_packages_cleanup: False
 #
 r_packages_updater: True
-r_package_updater_via_subversion: True
+r_package_updater_via_subversion: False
 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_package_updater_via_git: True
+r_package_updater_git_repo: 'https://code-repo.d4science.org/gCubeSystem/r-packages-list'
+r_packages_git_base_dir: /srv/r_updater
+r_packages_files_prefix: ''
 r_packages_updater_also_upgrades_installed_packages: False
 # They need to be flat text files
 # 1 package per line
@ -49,47 +54,39 @@ r_packages_updater_also_upgrades_installed_packages: False

 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
+  - r-base-core
+  - r-base-dev
+  - r-base-html
+  - r-mathlib
+
+r_distribution_required_packages:
+  - jags
+  - git
+  - subversion
+  - gdal-bin
+  - libgdal-dev
+  - libgeos-dev
+  - libspatialite-dev
+  - proj-bin
+  - proj-data
+  - libproj-dev
+  - libcurl4-openssl-dev
+  - texlive
+  - texlive-base
+  - texlive-binaries
+  - texlive-latex-base
+  - texlive-latex-extra
+  - texlive-formats-extra
+  - texlive-xetex
+  - libnetcdf-dev
+  - netcdf-bin

 # 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'
+r_plugins_packages_list: []

 # RHEL/CentOS:
 # http://springdale.princeton.edu/data/springdale/7/x86_64/os/Computational/
@ -113,30 +110,140 @@ r_base_packages_java_dev_el:

 r_distribution_required_el_packages: []

-r_cran_ubuntu_packages: []
+r_cran_ubuntu_packages:
+  - r-cran-abind
+  - r-cran-askpass
+  - r-cran-backports
+  - r-cran-base64enc
+  - r-cran-bayesplot
+  - r-cran-bh
+  - r-cran-boot
+  - r-cran-bslib
+  - r-cran-cachem
+  - r-cran-callr
+  - r-cran-checkmate
+  - r-cran-class
+  - r-cran-cli
+  - r-cran-cluster
+  - r-cran-coda
+  - r-cran-codetools
+  - r-cran-colorspace
+  - r-cran-colourpicker
+  - r-cran-commonmark
+  - r-cran-cpp11
+  - r-cran-crayon
+  - r-cran-crosstalk
+  - r-cran-curl
+  - r-cran-desc
+  - r-cran-digest
+  - r-cran-dplyr
+  - r-cran-dt
+  - r-cran-dygraphs
+  - r-cran-ellipsis
+  - r-cran-fansi
+  - r-cran-farver
+  - r-cran-fastmap
+  - r-cran-foreign
+  - r-cran-fs
+  - r-cran-generics
+  - r-cran-ggplot2
+  - r-cran-ggridges
+  - r-cran-glue
+  - r-cran-gridextra
+  - r-cran-gtable
+  - r-cran-gtools
+  - r-cran-htmltools
+  - r-cran-htmlwidgets
+  - r-cran-httpuv
+  - r-cran-igraph
+  - r-cran-inline
+  - r-cran-isoband
+  - r-cran-jquerylib
+  - r-cran-jsonlite
+  - r-cran-kernsmooth
+  - r-cran-labeling
+  - r-cran-later
+  - r-cran-lattice
+  - r-cran-lazyeval
+  - r-cran-lifecycle
+  - r-cran-littler
+  - r-cran-lme4
+  - r-cran-loo
+  - r-cran-magrittr
+  - r-cran-maptools
+  - r-cran-markdown
+  - r-cran-mass
+  - r-cran-matrix
+  - r-cran-matrixstats
+  - r-cran-mgcv
+  - r-cran-mime
+  - r-cran-miniui
+  - r-cran-minqa
+  - r-cran-munsell
+  - r-cran-nlme
+  - r-cran-nloptr
+  - r-cran-nnet
+  - r-cran-openssl
+  - r-cran-packrat
+  - r-cran-pillar
+  - r-cran-pkgbuild
+  - r-cran-pkgconfig
+  - r-cran-plyr
+  - r-cran-prettyunits
+  - r-cran-processx
+  - r-cran-promises
+  - r-cran-ps
+  - r-cran-purrr
+  - r-cran-r6
+  - r-cran-rappdirs
+  - r-cran-rcolorbrewer
+  - r-cran-rcpp
+  - r-cran-rcppeigen
+  - r-cran-rcppparallel
+  - r-cran-reshape2
+  - r-cran-rjags
+  - r-cran-rlang
+  - r-cran-rodbc
+  - r-cran-rpart
+  - r-cran-rprojroot
+  - r-cran-rsconnect
+  - r-cran-rstan
+  - r-cran-rstanarm
+  - r-cran-rstantools
+  - r-cran-rstudioapi
+  - r-cran-sass
+  - r-cran-scales
+  - r-cran-shiny
+  - r-cran-shinyjs
+  - r-cran-shinystan
+  - r-cran-shinythemes
+  - r-cran-sourcetools
+  - r-cran-sp
+  - r-cran-spatial
+  - r-cran-stanheaders
+  - r-cran-stringi
+  - r-cran-stringr
+  - r-cran-survival
+  - r-cran-svglite
+  - r-cran-sys
+  - r-cran-systemfonts
+  - r-cran-threejs
+  - r-cran-tibble
+  - r-cran-tidyselect
+  - r-cran-utf8
+  - r-cran-v8
+  - r-cran-vctrs
+  - r-cran-viridislite
+  - r-cran-withr
+  - r-cran-xfun
+  - r-cran-xtable
+  - r-cran-xts
+  - r-cran-yaml
+  - r-cran-zoo
+
 r_cran_install_from_sources: True
 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 }}' }
+#   - { name: 'robis', 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' }
--- a/tasks/main.yml
+++ b/tasks/main.yml
@ -2,9 +2,9 @@
 - import_tasks: r-packages_cleanup.yml
  when:
    - r_packages_cleanup
-    - ansible_distribution_file_variety == "Debian"
+    - ansible_distribution == "Ubuntu"
 - import_tasks: r-installation-deb.yml
-  when: ansible_distribution_file_variety == "Debian"
+  when: ansible_distribution == "Ubuntu"
 - import_tasks: r-installation-el.yml
  when: ansible_distribution_file_variety == "RedHat"
 - import_tasks: r-packages-install.yml
--- a/tasks/r-installation-deb.yml
+++ b/tasks/r-installation-deb.yml
@ -1,23 +1,53 @@
 ---
 - block:
-  - name: Add the cran repository key
-    apt_key: id={{ r_cran_repo_apt_key }} keyserver=keyserver.ubuntu.com state=present
-    tags: [ 'r_software', 'r_repo', 'r_repo_key' ]
+  - name: Add the CRAN repository (Ubuntu Trusty PPA)
+    apt_repository:
+      repo: '{{ r_cran_ubuntu_packages_ppa_trusty }}'
+      state: present
+      update_cache: yes

-  - name: Add the CRAN repository
-    apt_repository: repo='deb {{ r_cran_repo_url }}' state=present update_cache=yes
+  - name: Install some additional repositories. They provide dependencies for some R packages. Ubuntu Bionic
+    apt_repository:
+      repo: '{{ item }}'
+      state: present
+      update_cache: yes
+    loop: '{{ r_apt_additional_repos_trusty }}'

-  when: r_install_cran_repo
+  when:
+    - r_install_cran_repo
+    - ansible_distribution_version is version_compare('14.04', '==')
+  tags: [ 'r_software', 'r_repo' ]
+
+- block:
+  - name: Add the CRAN repository (Ubuntu Bionic PPA)
+    apt_repository:
+      repo: '{{ r_cran_ubuntu_packages_ppa }}'
+      state: present
+      update_cache: yes
+
+  - name: Install some additional repositories. They provide dependencies for some R packages. Ubuntu Bionic
+    apt_repository:
+      repo: '{{ item }}'
+      state: present
+      update_cache: yes
+    loop: '{{ r_apt_additional_repos }}'
+
+  when:
+    - r_install_cran_repo
+    - ansible_distribution_version is version_compare('18.04', '>=')
  tags: [ 'r_software', 'r_repo' ]

 - block:
  - name: Remove the CRAN repository
-    apt_repository: repo='deb {{ r_cran_repo_url }}' state=absent update_cache=yes
+    apt_repository:
+      repo: '{{ r_cran_ubuntu_packages_ppa }}'
+      state: absent
+      update_cache: yes

  when: not r_install_cran_repo
  tags: [ 'r_software', 'r_repo' ]

- block: 
+- block:
  - name: Remove the hold state from the debian R packages
    shell: apt-mark unhold {{ item }}
    with_items: '{{ r_base_packages_hold_list | default([]) }}'
@ -26,7 +56,10 @@
    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 }} update_cache=yes cache_valid_time=3600
+    apt:
+      pkg: '{{ r_base_packages_list }}'
+      state: '{{ r_packages_main_state }}'
+      cache_valid_time: 3600

  - name: When we install specific R deb packages, put them on hold
    shell: apt-mark hold {{ item }}
@ -36,17 +69,16 @@
    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
+    apt:
+      pkg: '{{ r_plugins_packages_list }}'
+      state: '{{ r_packages_state }}'
+      cache_valid_time: 3600

-  - 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
+    apt:
+      pkg: '{{ r_distribution_required_packages }}'
+      state: '{{ r_packages_state }}'
+      cache_valid_time: 3600
    tags: [ 'r_software', 'r_pkg', 'r_deps' ]

  tags: [ 'r_software', 'r_pkg' ]
--- a/tasks/r-packages-install.yml
+++ b/tasks/r-packages-install.yml
@ -1,9 +1,14 @@
 ---
 - block:
  - name: Configure the default CRAN mirror
-    template: src=Rprofile.site.j2 dest=/etc/R/Rprofile.site owner=root group=root mode=0444
+    template:
+      src: Rprofile.site.j2
+      dest: /etc/R/Rprofile.site
+      owner: root
+      group: root
+      mode: 0444
    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:
@ -14,18 +19,22 @@
    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
+    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: Add the Ubuntu PPA '{{ r_cran_ubuntu_packages_ppa }}'
-    apt_repository: repo='{{ r_cran_ubuntu_packages_ppa }}' state=present update_cache=yes
-
  - name: Install the R plugins from the Ubuntu PPA
-    apt: pkg={{ r_cran_ubuntu_packages }} state=present cache_valid_time=3600
+    apt:
+      pkg: '{{ r_cran_ubuntu_packages }}'
+      state: present
+      cache_valid_time: 3600

-  when: ansible_distribution_file_variety == "Debian"
+  when: ansible_distribution == "Ubuntu"
  tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_deb_plugins' ]

 - block:
@ -49,7 +58,7 @@
    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.
    command: >
      Rscript --slave --no-site-file --no-init-file --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 }}') { require(devtools); require(methods) ; install.packages('{{ r_source_plugins_dest_dir }}/{{ item.source }}', repos = NULL, type='source'); print('Added'); } else { print('Already Installed'); }"
--- a/tasks/r-packages-updater.yml
+++ b/tasks/r-packages-updater.yml
@ -1,4 +1,35 @@
 ---
+- name: Manage the subversion repository
+  block:
+    - name: Create the R packages updater SVN base directory
+      file:
+        dest: '{{ r_packages_svn_base_dir }}'
+        state: directory
+
+  when:
+    - r_cran_install_from_sources
+    - r_packages_updater
+    - r_package_updater_via_subversion
+  tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github', 'r_cran_pkgs', 'r_github_pkgs', 'r_packages_updater' ]
+
+- name: Manage the git repository of the packages lists
+  block:
+    - name: Remove the R packages updater SVN base directory
+      file:
+        dest: '{{ r_packages_svn_base_dir }}/RPackagesManagement'
+        state: absent
+
+    - name: Create the R packages updater git base directory
+      file:
+        dest: '{{ r_packages_git_base_dir }}'
+        state: directory
+
+  when:
+    - r_cran_install_from_sources
+    - r_packages_updater
+    - r_package_updater_via_git
+  tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github', 'r_cran_pkgs', 'r_github_pkgs', 'r_packages_updater' ]
+
 - block:
    - name: Install the R packages updater script
      template:
@ -8,11 +39,6 @@
        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"
--- a/templates/update_r_packages.sh.j2
+++ b/templates/update_r_packages.sh.j2
@ -18,13 +18,23 @@ TMP_FILES_DIR=/var/tmp/r_pkgs_update
 # We cannot answer questions
 DEBIAN_FRONTEND=noninteractive
 R_CRAN_MIRROR="{{ r_cran_mirror_site }}"
+{% if r_package_updater_via_git %}
+R_PKGS_FROM_SVN="False"
+R_PKGS_FROM_GIT="{{ r_package_updater_via_git }}"
+R_PKGS_DIR="r-packages-list"
+R_PKGS_URL="{{ r_package_updater_git_repo }}"
+R_PKGS_BASE_DIR="{{ r_packages_git_base_dir }}"
+GIT_UPDATE_STATUS=
+{% elif r_package_updater_via_subversion %}
 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"
+R_PKGS_FROM_GIT="False"
+R_PKGS_DIR=RPackagesManagement
+R_PKGS_URL="{{ r_package_updater_subversion_repo }}"
+R_PKGS_BASE_DIR="{{ r_packages_svn_base_dir }}"
 SVN_UPDATE_STATUS=
+{% endif %}
+R_PKGS_FILES_PREFIX="{{ r_packages_files_prefix }}"
+RSCRIPT_OPTIONS="--slave --no-site-file --no-init-file --no-save --no-restore-history"
 # In seconds. 60*60*6=21600s (6h)
 UPDATER_PROCESS_MAX_RUNTIME=21600
 # - debian packages list format:
@ -146,21 +156,39 @@ function get_data_files() {

 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
+    if [ -d $R_PKGS_BASE_DIR/$R_PKGS_DIR ] ; then
        logger "update_r_packages: SVN update"
-        cd $R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR
+        cd $R_PKGS_BASE_DIR/$R_PKGS_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
+        cd $R_PKGS_BASE_DIR
        logger "update_r_packages: first SVN checkout."
-        svn co $R_PKGS_SVN_URL >/dev/null 2>&1
+        svn co $R_PKGS_URL >/dev/null 2>&1
    fi
-    PKGS_LIST=$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/${R_PKGS_FILES_PREFIX}r_github_pkgs.txt
+    PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_deb_pkgs.txt
+    R_PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_cran_pkgs.txt
+    R_VERSIONED_PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_cran_versioned_pkgs.txt
+    R_PKGS_GITHUB=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_github_pkgs.txt
+}
+
+function get_data_files_from_git() {
+    logger "update_r_packages: files from a git repo."
+    if [ -d $R_PKGS_BASE_DIR/$R_PKGS_DIR ] ; then
+        logger "update_r_packages: git pull"
+        cd $R_PKGS_BASE_DIR/$R_PKGS_DIR
+        GIT_UPDATE_OP=$( git pull | tail -1 | grep Already  >/dev/null 2>&1 )
+        GIT_UPDATE_STATUS=$?
+    else
+        cd $R_PKGS_BASE_DIR
+        logger "update_r_packages: first git clone."
+        git clone $R_PKGS_URL >/dev/null 2>&1
+    fi
+    PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_deb_pkgs.txt
+    R_PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_cran_pkgs.txt
+    R_VERSIONED_PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_cran_versioned_pkgs.txt
+    R_PKGS_GITHUB=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_github_pkgs.txt
 }

 {% if ansible_distribution_file_variety == "Debian" %}
@ -174,9 +202,7 @@ function distribution_pkgs() {
            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
+        xargs -a $PKGS_LIST 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
        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"
@ -194,12 +220,6 @@ 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
@ -261,10 +281,10 @@ function r_github_pkgs() {
        for l in $( cat $R_PKGS_GITHUB ) ; do
            pkg=$( echo $l | cut -d "/" -f 2 )
            if [ "$ACTION" == "upgrade" ] ; then
-                Rscript $RSCRIPT_OPTIONS -e "require(devtools); require(methods); require(jsonlite) ; package_to_install <- '$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')"
+                Rscript $RSCRIPT_OPTIONS -e "require(devtools); require(methods); require(jsonlite) ; package_to_install <- '$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='false')"

            else
-                Rscript $RSCRIPT_OPTIONS -e "if (! ('$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') }"
+                Rscript $RSCRIPT_OPTIONS -e "if (! ('$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='false') }"
            fi
        done
    else
@ -279,7 +299,14 @@ function r_github_pkgs() {
 usage
 get_args
 init_env
-if [ $R_PKGS_FROM_SVN == 'True' ] ; then
+if [ $R_PKGS_FROM_GIT == 'True' ] ; then
+    get_data_files_from_git
+    if [ $GIT_UPDATE_STATUS -ne 1 -a "$ACTION" == "install" ] ; then
+        logger "update_r_packages: nothing new to install from git, exiting"
+        cleanup
+        exit 0
+    fi
+elif [ $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"