From a1a294669e13a0dee28c6139034a96d2abea41c1 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 1 Dec 2017 15:46:42 +0100
Subject: [PATCH] R packages updater: do not overlap the upgrade and install
 runs. Fix the job that kills old instances.

---
 R/tasks/r-packages-updater.yml      | 4 ++--
 R/templates/update_r_packages.sh.j2 | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/tasks/r-packages-updater.yml b/R/tasks/r-packages-updater.yml
index 2f09fd98..942e59b8 100644
--- a/R/tasks/r-packages-updater.yml
+++ b/R/tasks/r-packages-updater.yml
@@ -7,10 +7,10 @@
       file: dest={{ r_packages_svn_base_dir }} state=directory
 
     - name: Cron job that installs new R packages, if any
-      cron: name="install new R packages" user=root cron_file=install-r-packages minute="*/10" job="/usr/local/bin/update_r_packages install >/var/log/install_r_packages 2>&1" state=present
+      cron: name="install new R packages" user=root cron_file=install-r-packages minute="*/10" hour="5-0,1-2" job="/usr/local/bin/update_r_packages install >/var/log/install_r_packages 2>&1" state=present
 
     - name: Cron job that upgrades existing R packages and installs new ones, if any
-      cron: name="install new R packages" user=root cron_file=upgrade-r-packages hour="3" job="/usr/local/bin/update_r_packages upgrade >/var/log/update_r_packages 2>&1" state=present
+      cron: name="install new R packages" user=root cron_file=upgrade-r-packages minute="7" hour="3" job="/usr/local/bin/update_r_packages upgrade >/var/log/update_r_packages 2>&1" state=present
 
   when: r_packages_updater
   tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github', 'r_cran_pkgs', 'r_github_pkgs', 'r_packages_updater' ]
diff --git a/R/templates/update_r_packages.sh.j2 b/R/templates/update_r_packages.sh.j2
index 91e42ba7..4964943c 100644
--- a/R/templates/update_r_packages.sh.j2
+++ b/R/templates/update_r_packages.sh.j2
@@ -75,7 +75,7 @@ function fail() {
 function init_env() {
     if [ -f $LOCK_FILE ] ; then
         OLDPROC=$( cat $LOCK_FILE )
-        OLDPROC_RUNNING=$( ps auwwx |  grep -v grep | grep $OLDPROC )
+        OLDPROC_RUNNING=$( ps auwwx |  grep -v grep | grep $OLDPROC  | awk '{ print $2 }' )
         RETVAL=$?
         if [ $RETVAL -eq 0 ] ; then
             logger "update_r_packages: $OLDPROC_RUNNING"