update_r_packages.sh: remove the lock files that install.packages() fails to delete.

R/defaults/main.yml

@@ -16,9 +16,10 @@ r_install_cran_repo: absent
 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: 2.14.1
+r_base_pkg_version: 3.4.3
 r_packages_main_state: present
 r_packages_state: '{{ r_packages_main_state }}'
+r_sitelib_path: '/usr/local/lib/R/site-library'
 r_plugins_from_deb: True
 r_packages_cleanup: False
 #

R/tasks/r-packages-updater.yml

@@ -7,7 +7,7 @@
       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" hour="5-0,1-2" 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="5-23,1-2" 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 minute="7" hour="3" job="/usr/local/bin/update_r_packages upgrade >/var/log/update_r_packages 2>&1" state=present

R/templates/update_r_packages.sh.j2

@@ -163,6 +163,11 @@ function debian_pkgs() {
     fi
 }
 
+function remove_r_install_packages_lock_files() {
+    # install.packages leaves lock files around if the process crashes
+    rm -fr {{ r_sitelib_path }}/00LOCK-*
+    }
+
 function r_cran_pkgs() {
     if [ $CRAN_PKGS_SKIP -eq 0 ] ; then
         logger "update_r_packages: Installing R packages from CRAN"
@@ -221,6 +226,7 @@ else
     get_data_files
 fi
 debian_pkgs
+remove_r_install_packages_lock_files
 r_cran_pkgs
 r_github_pkgs
 cleanup