forked from ISTI-ansible-roles/ansible-roles
library/roles/R: script and cron job that downloads lists of debian and R packages and installs or upgrades them.
This commit is contained in:
Andrea Dell'Amico
parent
a3422e07fc
commit
f63a2231ff
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@ -21,6 +21,15 @@ r_packages_main_state: present
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r_packages_state: '{{ r_packages_main_state }}'
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r_plugins_from_deb: True
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r_packages_cleanup: False
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r_packages_updater: False
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# They need to be flat text files available via http
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# 1 package per line
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#r_debian_packages_list_url
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# package[:cran mirror]
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# The CRAN mirror URL is optional
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#r_cran_packages_list_url
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# user/package_name
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#r_github_packages_list_url
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r_source_plugins_dest_dir: /var/cache/R
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@ -2,3 +2,4 @@
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- include: r-packages_cleanup.yml
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when: r_packages_cleanup
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- include: r-installation.yml
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- include: r-packages-updater.yml
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@ -0,0 +1,27 @@
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---
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- block:
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- name: Install the R packages updater script
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template: src=update_r_packages.sh.j2 dest=/usr/local/bin/update_r_packages owner=root group=root mode=0755
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- name: Cron job that installs new R packages, if any
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cron: name="install new R packages" user=root cron_file=install-r-packages minute="*/10" job="/usr/local/bin/update_r_packages install" state=present
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- name: Cron job that upgrades existing R packages and installs new ones, if any
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cron: name="install new R packages" user=root cron_file=upgrade-r-packages hour="3" job="/usr/local/bin/update_r_packages upgrade" state=present
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when: r_packages_updater
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github', 'r_cran_pkgs', 'r_github_pkgs' ]
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- block:
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- name: Remove the R packages updater script
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file: dest=/usr/local/bin/update_r_packages state=absent
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- name: Remove the cron job that installs new R packages
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cron: name="install new R packages" user=root minute="*/10" cron_file=install-r-packages job="/usr/local/bin/update_r_packages install" state=absent
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- name: Remove the cron job that upgrades existing R packages and installs new ones
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cron: name="install new R packages" user=root cron_file=upgrade-r-packages hour="3" job="/usr/local/bin/update_r_packages upgrade" state=absent
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when: not r_packages_updater
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tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github', 'r_cran_pkgs', 'r_github_pkgs' ]
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@ -7,23 +7,6 @@
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#
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# NOTE: managed by ansible
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#
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# ## Example of .Rprofile
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# options(width=65, digits=5)
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# options(show.signif.stars=FALSE)
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# setHook(packageEvent("grDevices", "onLoad"),
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# function(...) grDevices::ps.options(horizontal=FALSE))
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# set.seed(1234)
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# .First <- function() cat("\n Welcome to R!\n\n")
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# .Last <- function() cat("\n Goodbye!\n\n")
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# ## Example of Rprofile.site
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# local({
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# # add MASS to the default packages, set a CRAN mirror
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# old <- getOption("defaultPackages"); r <- getOption("repos")
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# r["CRAN"] <- "http://my.local.cran"
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# options(defaultPackages = c(old, "MASS"), repos = r)
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#})
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local({r <- getOption("repos")
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r["CRAN"] <- "{{ r_cran_mirror_site }}"
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options(repos=r)
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@ -0,0 +1,177 @@
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#!/bin/bash
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RETVAl=
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PARAMS=$#
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ACTION=$1
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PROCNUM=$$
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OLDPROC=
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OLDPROC_RUNNING=
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LOCKDIR=/var/run
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LOCK_FILE=$LOCKDIR/.update_r_pkgs.lock
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TMP_FILES_DIR=/var/tmp/r_pkgs_update
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# We cannot answer questions
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DEBIAN_FRONTEND=noninteractive
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R_CRAN_MIRROR={{ r_cran_mirror_site }}
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# - debian packages list format:
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# one package per line
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DEB_PKGS_SKIP=0
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DEBIAN_PKGS_LIST_URL={{ r_debian_packages_list_url | default('') }}
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PKGS_LIST=
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# - R packages list format:
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# name[:mirror]
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CRAN_PKGS_SKIP=0
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R_PKGS_LIST_URL={{ r_cran_packages_list_url | default('') }}
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R_PKGS_LIST=
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# - R packages from github list format:
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# - owner/package
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GITHUB_PKGS_SKIP=0
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R_PKGS_FROM_GITHUB_LIST_URL={{ r_github_packages_list_url | default('') }}
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R_PKGS_GITHUB=
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trap "{ logger 'update_r_packages: trap intercepted, exiting.' ; cleanup ; exit 15 }" SIGHUP SIGINT SIGTERM
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function cleanup() {
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logger "update_r_packages: cleaning up"
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rm -f $LOCK_FILE
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rm -fr $TMP_FILES_DIR
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}
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function usage() {
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if [ $PARAMS -ne 1 ] ; then
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echo "Need at least an argument: 'upgrade' or 'install'."
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echo "- 'upgrade' installs new packages and upgrades the existin ones when needed."
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echo "- 'install' installs new packages."
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cleanup
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exit 1
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fi
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}
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function get_args() {
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if [ "$ACTION" != "upgrade" -a "$ACTION" != "install" ] ; then
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usage
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fi
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}
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function fail() {
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logger "Something went wrong, exiting."
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cleanup
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exit 1
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}
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function init_env() {
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if [ -f $LOCK_FILE ] ; then
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OLDPROC=$( cat $LOCK_FILE )
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OLDPROC_RUNNING=$( ps auwwx | grep -v grep | grep $OLDPROC )
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RETVAL=$?
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if [ $RETVAL -eq 0 ] ; then
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logger "update_r_packages: $OLDPROC_RUNNING"
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logger "update_r_packages: another process is running, exiting."
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exit 0
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else
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logger "update_r_packages: lock file exist but the process not. Continuing."
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rm -fr $TMP_FILES_DIR
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fi
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fi
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RETVAL=
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echo "$PROCNUM" > $LOCK_FILE
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mkdir -p $TMP_FILES_DIR
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}
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function get_data_files() {
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# Get the packages list
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if [ -z $DEBIAN_PKGS_LIST_URL ] ; then
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DEB_PKGS_SKIP=1
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logger "update_r_packages: the debian packages list is not available."
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else
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PKGS_LIST=$( mktemp $TMP_FILES_DIR/rdebs.XXXXXXX )
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logger "update_r_packages: getting the debian packages list."
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wget -q -o /dev/null -O $PKGS_LIST $DEBIAN_PKGS_LIST_URL
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fi
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if [ -z $R_PKGS_LIST_URL ] ; then
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CRAN_PKGS_SKIP=1
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logger "update_r_packages: the CRAN packages list is not available."
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else
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R_PKGS_LIST=$( mktemp $TMP_FILES_DIR/rpkgs.XXXXXXX )
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logger "update_r_packages: getting the R packages list that will be installed from CRAN"
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wget -q -o /dev/null -O $R_PKGS_LIST $R_PKGS_LIST_URL
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fi
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if [ -z $R_PKGS_FROM_GITHUB_LIST_URL ] ; then
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GITHUB_PKGS_SKIP=1
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logger "update_r_packages: the Github packages list is not available."
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else
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R_PKGS_GITHUB=$( mktemp $TMP_FILES_DIR/rpkgsgithub.XXXXXXX )
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logger "update_r_packages: getting the R packages list that will be installed from github"
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wget -q -o /dev/null -O $R_PKGS_GITHUB $R_PKGS_FROM_GITHUB_LIST_URL
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fi
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}
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function debian_pkgs() {
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if [ $DEB_PKGS_SKIP -eq 0 ] ; then
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# Update the apt cache and install the packages in non interactive mode
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logger "update_r_packages: Installing the debian dependencies"
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if [ -z "$(find /var/cache/apt/pkgcache.bin -mmin -360)" ]; then
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apt-get update -q >/dev/null 2>&1
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else
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logger "update_r_packages: APT cache not updated"
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fi
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xargs -a <(awk '/^\s*[^#]/' "$PKGS_LIST") -r -- apt-get install -q -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold"
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else
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logger "update_r_packages: skipping the debian packages installation"
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fi
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}
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function r_cran_pkgs() {
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if [ $CRAN_PKGS_SKIP -eq 0 ] ; then
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logger "update_r_packages: Installing R packages from CRAN"
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for l in $( cat $R_PKGS_LIST ) ; do
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pkg=$( echo $l | cut -d : -f 1 )
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is_mirror_ret=
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is_mirror=$( echo $l | grep ':' )
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is_mirror_ret=$?
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if [ $is_mirror_ret -eq 0 ] ; then
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mirror=$( echo $l | cut -d : -f 2 )
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else
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mirror=$R_CRAN_MIRROR
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fi
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if [ "$ACTION" == "upgrade" ] ; then
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Rscript --slave --no-save --no-restore-history -e "install.packages(pkgs='$pkg', repos=c('$mirror/'));"
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else
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Rscript --slave --no-save --no-restore-history -e "if (! ('$pkg' %in% installed.packages()[,'Package'])) { install.packages(pkgs='$pkg', repos=c('$mirror/')); }"
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fi
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done
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else
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logger "update_r_packages: skipping the R CRAN packages installation"
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fi
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}
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function r_github_pkgs() {
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if [ $GITHUB_PKGS_SKIP -eq 0 ] ; then
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logger "update_r_packages: Installing R packages from Github"
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for l in $( cat $R_PKGS_GITHUB ) ; do
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pkg=$( echo $l | cut -d "/" -f 2 )
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user=$( echo $l | cut -d "/" -f 1 )
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if [ "$ACTION" == "upgrade" ] ; then
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Rscript --slave --no-save --no-restore-history -e "require(devtools); require(methods); install_github('$l');"
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else
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Rscript --slave --no-save --no-restore-history -e "if (! ('$pkg' %in% installed.packages()[,'Package'])) { require(devtools); require(methods) ; install_github('$l'); }"
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fi
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done
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else
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logger "update_r_packages: skipping the R GitHub packages installation"
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fi
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}
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#########
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# Main
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#
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usage
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get_args
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init_env
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get_data_files
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debian_pkgs
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r_cran_pkgs
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r_github_pkgs
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cleanup
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exit 0
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